Isabel Birds

Isabel is a final year Natural Sciences undergraduate at the University of Leeds, studying Biology and Maths. She is currently exploring her interest in bioinformatics by carrying out a final year research project in our lab. In this project Isabel will be resolving nodes on the animal tree of life using a variety of methods and datasets. In particular Isabel has focussed on the chordate clade. She has been learning how to use high performance computing, how to script in UNIX and how to design computational biology experiments.

Please find the link to Isabels electronic appendix for her thesis here:

Appendix 1: List of genomes used and their Ensembl releases.

– AEDAE: Aedes aegypti (DB release: AaegL1; Ensembl v42; 26-NOV-2006)

– AMPQE: Amphimedon queenslandica (DB release: Ensembl Metazoa 12; Aqu1; 18-DEC-2011)

– ANAPL: Anas platyrhynchos (DB release: Ensembl 73; BGI_duck_1.0; 24-AUG-2013)

– ANOCA: Anolis carolinensis (DB release: Ensembl 70; AnoCar2.0; 11-DEC-2012)

– ANOGA: Anopheles gambiae (DB release: Ensembl 46; AgamP3; 4-AUG-2007)

– ASTMX: Astyanax mexicanus (DB release: Ensembl 74; AstMex102; 27-NOV-2013)

– BRAFL: Branchiostoma floridae (DB release: Brafl1)

– CAEBR: Caenorhabditis briggsae (DB release: Ensembl Metazoa 22; CB4; 13-MAR-2014)

– CAEEL: Caenorhabditis elegans (DB release: Ensembl 73; WBcel235; 24-AUG-2013)

– CAPTE: Capitella teleta (DB release: Ensembl Metazoa 27; GCA_000328365.1; 2-JUN-2015)

– CHICK: Gallus gallus (DB release: Ensembl 75; Galgal4; 7-FEB-2014)

– CHOHO: Choloepus hoffmanni (DB release: Ensembl 70; choHof1; 11-DEC-2012)

– CIOIN: Ciona intestinalis (DB release: Ensembl 70; KH; 11-DEC-2012)

– CIOSA: Ciona savignyi (DB release: Ensembl 70; CSAV2.0; 11-DEC-2012)

– DANPL: Danaus plexippus (DB release: Ensembl Metazoa 21; DanPle_1.0; 29-NOV-2013)

– DANRE: Danio rerio (DB release: Ensembl 80; GRCz10; 15-MAY-2015)

– DASNO: Dasypus novemcinctus (DB release: Ensembl 78; Dasnov3.0; 21-NOV-2014)

– DROME: Drosophila melanogaster (DB release: Ensembl 78; BDGP5; 21-NOV-2014)

– ECHTE: Echinops telfairi (DB release: Ensembl 70; TENREC; 11-DEC-2012)

– FICAL: Ficedula albicollis (DB release: Ensembl 73; FicAlb_1.4; 23-AUG-2013)

– GADMO: Gadus morhua (DB release: Ensembl 70; gadMor1; 11-DEC-2012)

– GASAC: Gasterosteus aculeatus (DB release: Ensembl 70; BROADS1; 12-DEC-2012)

– HELRO: Helobdella robusta (DB release: Version 1.0)

– HUMAN: Homo sapiens (DB release: Ensembl 80; GRCh38; 16-MAY-2015)

– LATCH: Latimeria chalumnae (DB release: Ensembl 70; LatCha1; 11-DEC-2012)

– LEPOC: Lepisosteus oculatus (DB release: Ensembl 74; LepOcu1; 27-NOV-2013)

– LOTGI: Lottia gigantea (DB release: Sbi1_4, Filtered Models)

– LOXAF: Loxodonta africana (DB release: Ensembl 70; loxAfr3; 11-DEC-2012)

– MACEU: Macropus eugenii (DB release: Ensembl 70; Meug_1.0; 11-DEC-2012)

– MELGA: Meleagris gallopavo (DB release: Ensembl 70; UMD2; 11-DEC-2012)

– MNELE: Mnemiopsis leidyi (DB release: Ensembl Metazoa 27; GCA_000226015.1; 2-JUN-2015)

– MONDO: Monodelphis domestica (DB release: Ensembl 80; BROADO5; 15-MAY-2015)

– MOUSE: Mus musculus (DB release: Ensembl 80; GRCm38; 16-MAY-2015)

– NOMLE: Nomascus leucogenys (DB release: Ensembl 80; Nleu1.0; 15-MAY-2015)

– ORENI: Oreochromis niloticus (DB release: Ensembl 67; Orenil1.0; 26-APR-2012)

– ORNAN: Ornithorhynchus anatinus (DB release: OANA5; Ensembl 49; 20-FEB-2008)

– ORYLA: Oryzias latipes (DB release: Ensembl 70; MEDAKA1; 11-DEC-2012)

– OTOGA: Otolemur garnettii (DB release: Ensembl 70; OtoGar3; 11-DEC-2012)

– PELSI: Pelodiscus sinensis (DB release: Ensembl 68; PelSin_1.0; 6-AUG-2012)

– POEFO: Poecilia formosa (DB release: Ensembl 77; PoeFor_5.1.2; 25-SEP-2014)

– PROCA: Procavia capensis (DB release: Ensembl 70; proCap1; 12-DEC-2012)

– SARHA: Sarcophilus harrisii (DB release: Ensembl 64; DEVIL7.0; 3-SEP-2011)

– STRPU: Strongylocentrotus purpuratus (DB release: Ensembl Metazoa 10; Spur2.5; 2-JUL 2011)

– TAEGU: Taeniopygia guttata (DB release: Ensembl 70; taeGut3.2.4; 12-DEC-2012)

– TAKRU: Takifugu rubripes (DB release: Ensembl 70; FUGU4; 11-DEC-2012)

– TETNG: Tetraodon nigroviridis (DB release: Ensembl 70; TETRAODON8; 11-DEC-2012)

– XENTR: Xenopus tropicalis (DB release: Ensembl 73; JGI_4.2; 23-AUG-2013)

– XIPMA: Xiphophorus maculatus (DB release: Ensembl 69; Xipmac4.4.2; 4-OCT-2012)

– CAEBR: Caenorhabditis briggsae (DB release: Ensembl Metazoa 22; CB4; 13-MAR-2014)

– CAEEL: Caenorhabditis elegans (DB release: Ensembl 73; WBcel235; 24-AUG-2013)

– DAPPU: Daphnia pulex (DB release: Frozen gene catalog, version 1.1)

– MYOLU: Myotis lucifugus (DB release: Ensembl 80; Myoluc2.0; 15-MAY-2015)

– NASVI: Nasonia vitripennis (DB release: Ensembl Metazoa 27; GCA_000002325.2; 2-JUN-2015)

– NEMVE: Nematostella vectensis (DB release: Nemve1)

– ONCVO: Onchocerca volvulus (DB release: Ensembl Metazoa 23; Cameroon_v3; 24-JUL-2014)

– PETMA: Petromyzon marinus (DB release: Ensembl 82; Pmarinus_7.0; 18-SEP-2015)

– PIGXX: Sus scrofa (DB release: Ensembl 80; Sscrofa10.2; 15-MAY-2015)

– RHOPR: Rhodnius prolixus (DB release: Ensembl Metazoa 27; RproC1; 2-JUN-2015)

– SCHMA: Schistosoma mansoni (DB release: Ensembl Metazoa 10; sma_v3.1; 2-JUL-2011)

– SORAR: Sorex araneus (DB release: Ensembl 70; COMMON_SHREW1; 11-DEC-2012)

– STRMM: Strigamia maritima (DB release: Ensembl Metazoa 25; Smar1; 18-DEC-2014)

– TETUR: Tetranychus urticae (DB release: Ensembl Metazoa 25; GCA_000239435.1; 18-DEC-2014)

– TRICA: Tribolium castaneum (DB release: Ensembl Metazoa 12; Tcas_3.0; 18-DEC-2011)

– TRISP: Trichinella spiralis (DB release: Ensembl Metazoa 13; Tspiralis1; 27-FEB-2012)

– ZOONE: Zootermopsis nevadensis (DB release: Ensembl Metazoa 25; GCA_000696155.1; 18-DEC-2014)

 

 

Appendix 2: List of species used for phylogenetic reconstruction.

ANAPL: Anas platyrhynchos. Duck MOUSE: Mus musculus. Mouse
ANOCA: Anolis carolinensis. Carolina Anole MYOLU: Myotis lucifugus. Bat
ASTMX: Astyanax mexicanus. Mexican Tetra NOMLE: Nomascus leucogenys. Gibbon
BRAFL: Branchiostoma floridae. Lanclet ORENI: Oreochromis niloticus. Nile Tilapia
CHICK: Gallus gallus. Red Junglefowl ORNAN: Ornithorhynchus anatinus. Platypus
CHOHO: Choloepus hoffmanni. Two-toed ORYLA: Oryzias latipes. Japanese Rice Fish
CIOIN: Ciona intestinalis. Vase Tunicate OTOGA: Otolemur garnettii. Galago
CIOSA: Ciona savignyi. Solitary Sea Squirt PELSI: Pelodiscus sinensis. Chinese softshell turtle
DANRE: Danio rerio. Zebrafish PETMA: Petromyzon marinus. Sea Lamprey
DASNO: Dasypus novemcinctus. Armadillo PIGXX: Sus scrofa. Pig
ECHTE: Echinops telfairi. Lesser Hedgehog Tenrec POEFO: Poecilia Formosa. Amazon Molly
FICAL: Ficedula albicollis. Flycatcher PROCA: Procavia capensis. Hyrax
GADMO: Gadus morhua. Atlantic cod SARHA: Sarcophilus harrisii. Tasmanian Devil
GASAC: Gasterosteus aculeatus. Three Spined Stickleback SORAR: Sorex araneus. Common Shrew
HUMAN: Homo sapiens. Human STRPU: Strongylocentrotus purpuratus. Purple Sea Urchin
LATCH: Latimeria chalumnae. Coelacanth TAEGU: Taeniopygia guttata. Zebra Finch
LEPOC: Lepisosteus oculatus Spotted Gar TAKRU: Takifugu rubripes. Japanese Puffer Fish
LOXAF: Loxodonta Africana. Elephant TETNG: Tetraodon nigroviridis. Green Spotted Puffer Fish
MACEU: Macropus eugenii. Wallaby XENTR: Xenopus tropicalis. Western Clawed Frog
MELGA: Meleagris gallopavo. Turkey XIPMA: Xiphophorus maculatus. Southern Platyfish
MONDO: Monodelphis domestica. Opossum  

 

 


Appendix 3: Orthologous groups used in phylogenetic reconstruction, and their members.

The groups of orthologs are given as one per row, starting with a group identifier, followed by all group members, all separated by tabs.

OMA00018      ANAPL:ENSAPLG00000011251         ANOCA:ENSACAG00000002067       ASTMX:ENSAMXG00000017072        CAEEL:CAM84806.1; CAR64665.1; F15G9.4            CHICK:ENSGALG00000005141          CHOHO:ENSCHOG00000004310        CIOIN:ENSCING00000007725            DANRE:ENSDARG00000016936         DASNO:ENSDNOG00000014896        ECHTE:ENSETEG00000017569           FICAL:ENSFALG00000003249            GADMO:ENSGMOG00000010733       GASAC:ENSGACG00000007309       HUMAN:AAK68690.1; BAB71154.1; BAB71216.1; CAC37630.1; CAH74051.1; CAI17844.1; CAI17853.1; CAI17854.1; CAI17858.1; CAI17864.1; CAI17865.1; CAI17871.1; ENSG00000143341            LATCH:ENSLACG00000013130         LEPOC:ENSLOCG00000001656          MACEU:ENSMEUG00000010967         MELGA:ENSMGAG00000001182            MONDO:ENSMODG00000011458       MOUSE:ENSMUSG00000066842        MYOLU:MYOLU05707 | ENSMLUP00000015439 | ENSMLUT00000016938 | ENSMLUG00000016911 | G1PVR0_MYOLU | hemicentin 1 [Source:HGNC Symbol;Acc:HGNC:19194]       NOMLE:ENSNLEG00000018033            ORENI:ENSONIG00000009997            ORNAN:ENSOANG00000001016        ORYLA:ENSORLG00000009600        OTOGA:ENSOGAG00000014105            PELSI:ENSPSIG00000014198  POEFO:ENSPFOG00000011299          PROCA:ENSPCAG00000008408         STRPU:SPU_011693gn            TAEGU:ENSTGUG00000003617         TAKRU:ENSTRUG00000005508         XENTR:ENSXETG00000017411          XIPMA:ENSXMAG00000002326

OMA00023      AMPQE:Aqu1.221214 ANAPL:ENSAPLG00000008642         ASTMX:ENSAMXG00000013364        CAPTE:CapteG219707; ELU01149; ELU01149.1     CHOHO:ENSCHOG00000006207        CIOIN:ENSCING00000004793  CIOSA:ENSCSAVG00000002254       DANRE:ENSDARG00000029482            DASNO:ENSDNOG00000002408        ECHTE:ENSETEG00000018825           FICAL:ENSFALG00000012264           GADMO:ENSGMOG00000003131            GASAC:ENSGACG00000016262       HUMAN:AAC23748.2; AAF75819.1; AAS47698.1; CAH70620.1; CAH70621.1; CAH71587.1; CAH71588.1; CAH73621.1; CAI19189.1; CAI23041.1; ENSG00000042781 LEPOC:ENSLOCG00000016044          LOTGI:e_gw1.29.81.1 MACEU:ENSMEUG00000008627            MELGA:ENSMGAG00000009443        MONDO:ENSMODG00000004113       MOUSE:AAF70550.1; AAZ23164.1; ENSMUSG00000026609            NOMLE:ENSNLEG00000014249          ORENI:ENSONIG00000017156            OTOGA:ENSOGAG00000014786       PELSI:ENSPSIG00000005976            POEFO:ENSPFOG00000015537          PROCA:ENSPCAG00000015160         STRPU:SPU_017733gn           TAEGU:ENSTGUG00000002871            TAKRU:ENSTRUG00000001783         XENTR:ENSXETG00000020925          XIPMA:ENSXMAG00000017603

OMA00041      ANAPL:ENSAPLG00000015036         ANOCA:ENSACAG00000005966       ASTMX:ENSAMXG00000024718            DANRE:ENSDARG00000097827         DASNO:ENSDNOG00000025390        DROME:FBgn0053087 FICAL:ENSFALG00000000309            GASAC:ENSGACG00000000618       HUMAN:AAC64265.1; AAH45107.1; ABC40732.1; CAA32112.1; CAA33464.1; CAD57169.1; ENSG00000123384     LATCH:ENSLACG00000018537         LEPOC:ENSLOCG00000006089          LOXAF:ENSLAFG00000005976            MACEU:ENSMEUG00000003168         MOUSE:ENSMUSG00000040249        ORENI:ENSONIG00000019160            ORYLA:ENSORLG00000015478            OTOGA:ENSOGAG00000012030       POEFO:ENSPFOG00000003159          PROCA:ENSPCAG00000014030         SARHA:ENSSHAG00000007379            STRPU:SPU_020978gn           TAEGU:ENSTGUG00000015747         TAKRU:ENSTRUG00000008762         TETNG:ENSTNIG00000014562            XENTR:ENSXETG00000010934          XIPMA:ENSXMAG00000009715

OMA00048      AMPQE:Aqu1.228853 ANOCA:ENSACAG00000004234       ASTMX:ENSAMXG00000013105        CAPTE:CapteG226634; ELT88649; ELT88649.1     CIOIN:ENSCING00000007623  DANRE:ENSDARG00000016782         DAPPU:DAPPU03331 | NCBI_GNO_0800168 | NCBI_GNO_0800168 | E9G229_DAPPU | jgi|Dappu1|313219|NCBI_GNO_0800168    DASNO:ENSDNOG00000015098        DROME:FBgn0030674 ECHTE:ENSETEG00000004454            GADMO:ENSGMOG00000008327       GASAC:ENSGACG00000008789       HELRO:81131  HUMAN:AAC62492.1; AAF28950.1; AAH02602.2; AAH63505.1; AAV90838.1; AAX24125.1; AAY98258.1; BAA20771.3; BAB13404.1; BAC06833.1; CAB82393.1; CAG33094.1; CAI39580.1; CAI42354.1; CAI42654.1; EAW93161.1; EAW93166.1; ENSG00000086758          LATCH:ENSLACG00000010403         LEPOC:ENSLOCG00000014797            LOXAF:ENSLAFG00000014785         MACEU:ENSMEUG00000011796         MONDO:ENSMODG00000020890       MOUSE:ENSMUSG00000025261            MYOLU:MYOLU09735 | ENSMLUP00000000196 | ENSMLUT00000000214 | ENSMLUG00000000179 | G1NSS6_MYOLU | HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:HGNC:30892]   NEMVE:NEMVE01929 | 30016 | gw.39.113.1 | jgi|Nemve1|30016|gw.39.113.1           NOMLE:ENSNLEG00000016017          ORENI:ENSONIG00000012021            ORNAN:ENSOANG00000000714            OTOGA:ENSOGAG00000001999       PIGXX:PIGXX18815 | ENSSSCP00000019874 | ENSSSCT00000032330 | ENSSSCG00000012328 | I3L770_PIG | HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:HGNC:30892]   POEFO:ENSPFOG00000010355            PROCA:ENSPCAG00000008911         SARHA:ENSSHAG00000001097        SORAR:SORAR10655 | ENSSARP00000009605 | ENSSART00000010633 | ENSSARG00000010460 | HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:30892]            STRPU:SPU_027523gn           TAKRU:ENSTRUG00000014610         TETNG:ENSTNIG00000015085            TETUR:TETUR06762 | tetur15g03010.1 | tetur15g03010 | T1KMV4_TETUR        TRICA:TRICA00180 | TCOGS2:TC004152-PA | TCOGS2:TC004152-RA | EFA10984 | TCOGS2:TC004152 | D6W6Q2_TRICA          XENTR:ENSXETG00000030011          XIPMA:ENSXMAG00000010828

OMA00083      AEDAE:AAEL000512  ANOCA:ENSACAG00000000566       ANOGA:AGAP003226            CAPTE:CapteG211041; ELU14607; ELU14607.1            DANPL:KGM_21512    DANRE:ENSDARG00000000606         DASNO:ENSDNOG00000006650        DROME:FBgn0013809 HUMAN:AAC50700.1; AAH15442.1; AAI04885.1; AAI13425.1; AAI17260.1; AAI43667.1; AAX93108.1; AAX93115.1; AAY24108.1; BAB15685.1; BAB21788.2; BAC04400.1; CAA10559.1; CAC21651.1; EAW99557.1; ENSG00000115423         LEPOC:ENSLOCG00000012784          LOTGI:estExt_Genewise1.C_sca_2710014            LOXAF:ENSLAFG00000009483         MOUSE:ENSMUSG00000052861        MYOLU:MYOLU12322 | ENSMLUP00000004015 | ENSMLUT00000004412 | ENSMLUG00000004395 | G1P2C9_MYOLU | dynein, axonemal, heavy chain 6 [Source:HGNC Symbol;Acc:HGNC:2951] NASVI:NASVI00796 | NV13281-PA | NV13281-RA | NV13281 | K7IW21_NASVI    NEMVE:NEMVE14184 | 175144 | estExt_gwp.C_3640015 | A7SWW2_NEMVE | jgi|Nemve1|175144|estExt_gwp.C_3640015   NOMLE:ENSNLEG00000001321          OTOGA:ENSOGAG00000011781       PELSI:ENSPSIG00000011426            PETMA:PETMA02857 | ENSPMAP00000008577 | ENSPMAT00000008615 | ENSPMAG00000007744 | S4RTN7_PETMA | dynein, axonemal, heavy polypeptide 7 like [Source:ZFIN;Acc:ZDB-GENE-030616-623]           RHOPR:RHOPR14961 | RPRC008889-PA | RPRC008889-RA | RPRC008889 | T1HXW9_RHOPR        SARHA:ENSSHAG00000000475        SCHMA:SCHMA07895 | Smp_130810__mRNA | CAZ29284 | Smp_130810 | Putative uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:C4Q1G0]  STRMM:STRMM14271 | SMAR008528-PA | SMAR008528-RA | SMAR008528 | T1J4J2_STRMM           STRPU:SPU_004934gn           TRICA:TRICA11755 | TCOGS2:TC000119-PA | TCOGS2:TC000119-RA | EEZ99537 | TCOGS2:TC000119 | D6WDA6_TRICA

OMA00098      ANAPL:ENSAPLG00000011764         ANOCA:ENSACAG00000000960       ASTMX:ENSAMXG00000008974            BRAFL:estExt_fgenesh2_pg.C_170060         CAPTE:CapteG205240; ELU16777; ELU16777.1        CHICK:ENSGALG00000006829            CHOHO:ENSCHOG00000007811        DANRE:ENSDARG00000054570         DASNO:ENSDNOG00000016471        FICAL:ENSFALG00000014047            GADMO:ENSGMOG00000012395       GASAC:ENSGACG00000004970       HUMAN:AAA86535.2; AAK00511.1; AAK58892.1; AAM73708.1; BAA24851.2; BAB70696.1; ENSG00000157106        LATCH:ENSLACG00000008522         LEPOC:ENSLOCG00000007061            LOTGI:estExt_fgenesh2_pg.C_sca_80241    LOXAF:ENSLAFG00000018634         MELGA:ENSMGAG00000007757            MONDO:ENSMODG00000006102       MOUSE:BAC30884.2; BAC33168.2; BAC33729.1; BAC34941.1; BAC97946.1; BAD90238.1; ENSMUSG00000030655         MYOLU:MYOLU13048 | ENSMLUP00000005229 | ENSMLUT00000005722 | ENSMLUG00000005675 | G1P5E7_MYOLU | SMG1 phosphatidylinositol 3-kinase-related kinase [Source:HGNC Symbol;Acc:HGNC:30045]       NASVI:NASVI00522 | NV17224-PA | NV17224-RA | NV17224 | K7J769_NASVI           ORENI:ENSONIG00000003445            ORNAN:ENSOANG00000012229        OTOGA:ENSOGAG00000013206            PELSI:ENSPSIG00000004543  POEFO:ENSPFOG00000015433          PROCA:ENSPCAG00000002964         SARHA:ENSSHAG00000017370            SORAR:SORAR08246 | ENSSARP00000011636 | ENSSART00000012883 | ENSSARG00000012856 | smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans) [Source:HGNC Symbol;Acc:30045]        STRPU:SPU_016754gn           TAEGU:ENSTGUG00000009449            XIPMA:ENSXMAG00000010144          ZOONE:ZOONE08887 | KDR12657 | L798_13316 | A0A067R3Y6_ZOONE

OMA00110      ANAPL:ENSAPLG00000002327         ANOCA:ENSACAG00000008238       ASTMX:ENSAMXG00000004340            CHICK:ENSGALG00000000713          DANRE:ENSDARG00000103057         DASNO:ENSDNOG00000046047        ECHTE:ENSETEG00000014223            FICAL:ENSFALG00000002706           GADMO:ENSGMOG00000002909       GASAC:ENSGACG00000015779       HUMAN:AAC14462.1; AAC31674.1; AAC79153.1; BAA01095.1; EAW59168.1; EAW59170.1; ENSG00000140836           LATCH:ENSLACG00000015046            LEPOC:ENSLOCG00000004206          LOXAF:ENSLAFG00000017476         MELGA:ENSMGAG00000008764        MOUSE:ENSMUSG00000038872            MYOLU:MYOLU06635 | ENSMLUP00000014682 | ENSMLUT00000016116 | ENSMLUG00000016100 | G1PTV6_MYOLU | zinc finger homeobox 3 [Source:HGNC Symbol;Acc:HGNC:777]          ORNAN:ENSOANG00000005084        ORYLA:ENSORLG00000007874        PIGXX:PIGXX13669 | ENSSSCP00000002970 | ENSSSCT00000003049 | ENSSSCG00000002752 | F1S397_PIG | zinc finger homeobox 3 [Source:HGNC Symbol;Acc:HGNC:777]            POEFO:ENSPFOG00000001702          PROCA:ENSPCAG00000010600         SARHA:ENSSHAG00000014394        STRPU:SPU_017348gn            TAEGU:ENSTGUG00000008190         TAKRU:ENSTRUG00000017601         XENTR:ENSXETG00000023509

OMA00194      AEDAE:AAEL008371  ANAPL:ENSAPLG00000014612; EOB00234.1           CAPTE:CapteG172215; ELT88415            CHICK:ENSGALG00000005660          CHOHO:ENSCHOG00000008564        DAPPU:DAPPU07843 | PASA_GEN_5900030 | PASA_GEN_5900030 | E9H0M4_DAPPU | jgi|Dappu1|307021|PASA_GEN_5900030   DASNO:ENSDNOG00000014464        DROME:FBgn0015269 ECHTE:ENSETEG00000003433            FICAL:ENSFALG00000004959           GADMO:ENSGMOG00000015388       HELRO:117118            HUMAN:AAA18483.1; AAA59921.1; AAA59922.1; AAA59923.1; AAA59924.1; AAA59925.1; AAA59928.1; AAA74897.1; AAB24636.1; AAB48373.1; AAB48374.1; AAB48375.1; AAB48376.1; AAB48377.1; AAB48378.1; AAB48379.1; AAB48380.1; AAB59558.1; AAV50004.1; BAA01371.1; BAA02150.1; BAA07669.1; CAA69179.1; EAW80272.1; EAW80275.1; ENSG00000196712      LATCH:ENSLACG00000017003         LEPOC:ENSLOCG00000004716          LOTGI:e_gw1.2.786.1            LOXAF:ENSLAFG00000000258         MELGA:ENSMGAG00000008314        MONDO:ENSMODG00000019215       MOUSE:AAA39806.1; AAA68132.1; BAA06395.1; BAA06396.1; CAA38690.1; ENSMUSG00000020716  MYOLU:MYOLU09308 | ENSMLUP00000005804 | ENSMLUT00000006354 | ENSMLUG00000006320 | G1P6U7_MYOLU | neurofibromin 1 [Source:HGNC Symbol;Acc:HGNC:7765]     NASVI:NASVI15159 | NV15474-PA | NV15474-RA | NV15474 | K7J294_NASVI    NOMLE:ENSNLEG00000010582          ORENI:ENSONIG00000014832            ORYLA:ENSORLG00000015104            PELSI:ENSPSIG00000017227  PIGXX:PIGXX03273 | ENSSSCP00000018804 | ENSSSCT00000019317 | AAC77495.1 | ENSSSCG00000017748 | F1RJ58_PIG | Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:I3LV00]      POEFO:ENSPFOG00000004914          PROCA:ENSPCAG00000010964            RHOPR:RHOPR13919 | RPRC009491-PA | RPRC009491-RA | RPRC009491 | T1HZM1_RHOPR         SARHA:ENSSHAG00000018926            SORAR:SORAR11793 | ENSSARP00000004140 | ENSSART00000004552 | ENSSARG00000004453 | neurofibromin 1 [Source:HGNC Symbol;Acc:7765]       STRMM:STRMM12588 | SMAR009214-PA | SMAR009214-RA | SMAR009214 | T1J6E5_STRMM      STRPU:SPU_017904gn            TAEGU:ENSTGUG00000008487         TAKRU:ENSTRUG00000005831         TETNG:ENSTNIG00000004988            TETUR:TETUR15077 | tetur02g01260.1 | tetur02g01260 | T1JUK4_TETUR    XENTR:ENSXETG00000021350          XIPMA:ENSXMAG00000012244

OMA00205      AEDAE:AAEL005930  AMPQE:Aqu1.223821 ANAPL:ENSAPLG00000004191         ANOCA:ENSACAG00000008995            ASTMX:ENSAMXG00000020014        BRAFL:fgenesh2_pg.scaffold_385000018    CAPTE:CapteG219094; ELT92482; ELT92482.1            CHICK:ENSGALG00000016045          CHOHO:ENSCHOG00000013701        CIOIN:ENSCING00000008630  DANPL:KGM_10406            DANRE:ENSDARG00000018192         DAPPU:DAPPU05611 | e_gw1.20.116.1 | e_gw1.20.116.1 | E9GFI3_DAPPU | jgi|Dappu1|49748|e_gw1.20.116.1            DASNO:ENSDNOG00000007897        DROME:FBgn0002431 ECHTE:ENSETEG00000020339           FICAL:ENSFALG00000005901            GADMO:ENSGMOG00000018440       GASAC:ENSGACG00000004642       HELRO:71154  HUMAN:AAD01259.2; AAF88143.1; AAI37235.1; BAA74919.3; ENSG00000104517      LATCH:ENSLACG00000012137         LEPOC:ENSLOCG00000009882          LOTGI:e_gw1.67.155.1            MELGA:ENSMGAG00000012296        MONDO:ENSMODG00000005976       MOUSE:ENSMUSG00000037487        MYOLU:MYOLU07967 | ENSMLUP00000007430 | ENSMLUT00000008139 | ENSMLUG00000008052 | G1PAU3_MYOLU | ubiquitin protein ligase E3 component n-recognin 5 [Source:HGNC Symbol;Acc:HGNC:16806]      NASVI:NASVI16757 | NV12709-PA | NV12709-RA | NV12709 | K7IUF4_NASVI            NOMLE:ENSNLEG00000003404          ONCVO:ONCVO11002 | OVOC1830 | WBGene00238639 | A0A044S6F6_ONCVO            ORENI:ENSONIG00000016431            ORYLA:ENSORLG00000003009        OTOGA:ENSOGAG00000004491       PELSI:ENSPSIG00000013244            POEFO:ENSPFOG00000012957          PROCA:ENSPCAG00000001160         RHOPR:RHOPR14589 | RPRC005792-PA | RPRC005792-RA | RPRC005792 | T1HP18_RHOPR          SARHA:ENSSHAG00000017701        SCHMA:SCHMA04856 | Smp_150360__mRNA | CAZ32803 | Smp_150360 | Ubiquitin–protein ligase edd, putative [Source:UniProtKB/TrEMBL;Acc:C4QBG8]     STRMM:STRMM11890 | SMAR011626-PA | SMAR011626-RA | SMAR011626 | T1JCV6_STRMM         STRPU:SPU_011574gn           TAEGU:ENSTGUG00000012099         TETNG:ENSTNIG00000013292            TETUR:TETUR07044 | tetur14g01790.1 | tetur14g01790 | T1KLA9_TETUR    TRICA:TRICA04420 | TCOGS2:TC014081-PA | TCOGS2:TC014081-RA | EFA03940 | TCOGS2:TC014081         XENTR:ENSXETG00000031995          XIPMA:ENSXMAG00000002429          ZOONE:ZOONE13239 | KDR11630 | L798_13956 | A0A067QPQ4_ZOONE

OMA00239      ASTMX:ENSAMXG00000015567        BRAFL:estExt_fgenesh2_pg.C_210009         DANRE:ENSDARG00000018566            DAPPU:DAPPU03216 | estExt_Genewise1.C_80108 | estExt_Genewise1.C_80108 | E9G2W4_DAPPU | jgi|Dappu1|208250|estExt_Genewise1.C_80108        GADMO:ENSGMOG00000018206       GASAC:ENSGACG00000010114       NASVI:NASVI16142 | NV13706-PA | NV13706-RA | NV13706 | K7IX85_NASVI       NEMVE:NEMVE23302 | 239614 | estExt_fgenesh1_pg.C_170047 | A7RNL3_NEMVE | jgi|Nemve1|239614|estExt_fgenesh1_pg.C_170047   ORENI:ENSONIG00000008549            ORYLA:ENSORLG00000004247            POEFO:ENSPFOG00000011440          STRPU:SPU_017634gn           TAKRU:ENSTRUG00000016964         TETNG:ENSTNIG00000016020            TRICA:TRICA00437 | TCOGS2:TC005186-PA | TCOGS2:TC005186-RA | EFA11221 | TCOGS2:TC005186   XIPMA:ENSXMAG00000016525

OMA00254      ANAPL:ENSAPLG00000014792; EOB06522.1           ANOCA:ENSACAG00000017937       ANOGA:AGAP010088            ASTMX:ENSAMXG00000002577        BRAFL:estExt_gwp.C_70636 CAPTE:CapteG183046; ELU17500; ELU17500.1            CHICK:ENSGALG00000016236          CIOSA:ENSCSAVG00000008942       DANPL:KGM_15881    DANRE:ENSDARG00000013708            DAPPU:DAPPU16970 | PASA_GEN_5500012 | PASA_GEN_5500012 | E9GZ89_DAPPU | jgi|Dappu1|306876|PASA_GEN_5500012            DASNO:ENSDNOG00000008295        DROME:FBgn0005632 ECHTE:ENSETEG00000003732           FICAL:ENSFALG00000001538            GADMO:ENSGMOG00000012935       GASAC:ENSGACG00000002025       HUMAN:AAC25395.1; CAA66942.1; CAD13527.2; CAD18900.2; ENSG00000124486     LATCH:ENSLACG00000002469         LEPOC:ENSLOCG00000002227          LOTGI:estExt_Genewise1Plus.C_sca_230259            LOXAF:ENSLAFG00000008552         MELGA:ENSMGAG00000014611        MONDO:ENSMODG00000021098       MOUSE:AAY99447.1; ENSMUSG00000031010         MYOLU:MYOLU06152 | ENSMLUP00000009287 | ENSMLUT00000010190 | AEI55856.1 | ENSMLUG00000010139 | G1PFE4_MYOLU | ubiquitin specific peptidase 9, X-linked [Source:HGNC Symbol;Acc:HGNC:12632]          NASVI:NASVI03020 | NV11605-PA | NV11605-RA | NV11605 | K7IRB1_NASVI    NOMLE:ENSNLEG00000001837          ORENI:ENSONIG00000006851            ORNAN:ENSOANG00000011275            ORYLA:ENSORLG00000010762        OTOGA:ENSOGAG00000027364       PELSI:ENSPSIG00000007248  POEFO:ENSPFOG00000014198            PROCA:ENSPCAG00000013682         SARHA:ENSSHAG00000008762        SORAR:SORAR07840 | ENSSARP00000012658 | ENSSART00000014003 | ENSSARG00000013975 | ubiquitin specific peptidase 9, X-linked [Source:HGNC Symbol;Acc:12632]       STRMM:STRMM08682 | SMAR006759-PA | SMAR006759-RA | SMAR006759 | T1IZS4_STRMM   STRPU:SPU_002851gn           TAEGU:ENSTGUG00000006522         TAKRU:ENSTRUG00000013707            TETNG:ENSTNIG00000014968            TETUR:TETUR12022 | tetur06g04700.1 | tetur06g04700 | T1K7L3_TETUR     TRICA:TRICA04629 | TCOGS2:TC010455-PA | TCOGS2:TC010455-RA | EFA03030 | TCOGS2:TC010455 XENTR:ENSXETG00000015489          XIPMA:ENSXMAG00000018028            ZOONE:ZOONE05091 | KDR24425 | L798_05086 | A0A067RUD8_ZOONE

OMA00255      AEDAE:AAEL006187  ANAPL:ENSAPLG00000010927         ANOCA:ENSACAG00000003819       ANOGA:AGAP001700            BRAFL:estExt_fgenesh2_pg.C_720016         CHICK:ENSGALG00000007276          CIOIN:ENSCING00000008541  CIOSA:ENSCSAVG00000011812            DANPL:KGM_13538    DANRE:ENSDARG00000058419         DROME:FBgn0039959 FICAL:ENSFALG00000007644            GADMO:ENSGMOG00000017702       GASAC:ENSGACG00000013560       HELRO:107160            HUMAN:ENSG00000089154            LATCH:ENSLACG00000018421         LOTGI:estExt_Genewise1Plus.C_sca_920144          LOXAF:ENSLAFG00000012272            MACEU:ENSMEUG00000016364         MELGA:ENSMGAG00000008798        MONDO:ENSMODG00000015221       MOUSE:ENSMUSG00000041638            MYOLU:MYOLU09921 | ENSMLUP00000014102 | ENSMLUT00000015478 | ENSMLUG00000015444 | G1PSF5_MYOLU | GCN1 general control of amino-acid synthesis 1-like 1 (yeast) [Source:HGNC Symbol;Acc:HGNC:4199]        NASVI:NASVI02870 | NV17620-PA | NV17620-RA | NV17620 | K7J8A6_NASVI           NOMLE:ENSNLEG00000000276          ORENI:ENSONIG00000015992            ORYLA:ENSORLG00000018601            OTOGA:ENSOGAG00000001952       PELSI:ENSPSIG00000014426  POEFO:ENSPFOG00000006849          PROCA:ENSPCAG00000016143            RHOPR:RHOPR06770 | RPRC004279-PA | RPRC004279-RA | RPRC004279 | T1HJQ7_RHOPR         SARHA:ENSSHAG00000018556            SORAR:SORAR09004 | ENSSARP00000006018 | ENSSART00000006632 | ENSSARG00000006491 | GCN1 general control of amino-acid synthesis 1-like 1 (yeast) [Source:HGNC Symbol;Acc:4199]     STRMM:STRMM14017 | SMAR007809-PA | SMAR007809-RA | SMAR007809 | T1J2L3_STRMM            STRPU:SPU_028779gn           TAEGU:ENSTGUG00000009369         TAKRU:ENSTRUG00000016061         TETNG:ENSTNIG00000011458            TETUR:TETUR01225 | tetur37g01130.1 | tetur37g01130 | T1L480_TETUR     XENTR:ENSXETG00000012193          XIPMA:ENSXMAG00000003953            ZOONE:ZOONE10869 | KDR23119 | L798_15201 | A0A067RTH7_ZOONE

OMA00277      ANAPL:ENSAPLG00000011964         ANOCA:ENSACAG00000012846       ASTMX:ENSAMXG00000002382            CHICK:ENSGALG00000001732          DANRE:ENSDARG00000059846         DROME:FBgn0038651 FICAL:ENSFALG00000008862            GADMO:ENSGMOG00000011318       GASAC:ENSGACG00000009739       HUMAN:AAI30615.1; BAB13458.1; BAB14689.1; ENSG00000152223            LEPOC:ENSLOCG00000006481          LOXAF:ENSLAFG00000002464         MACEU:ENSMEUG00000009791         MELGA:ENSMGAG00000001532            MOUSE:BAC65818.1; ENSMUSG00000039840          MYOLU:MYOLU02563 | ENSMLUP00000008941 | ENSMLUT00000009807 | ENSMLUG00000009791 | G1PEJ4_MYOLU | ectopic P-granules autophagy protein 5 homolog (C. elegans) [Source:HGNC Symbol;Acc:HGNC:29331]            NOMLE:ENSNLEG00000010921          ORENI:ENSONIG00000013677            ORNAN:ENSOANG00000014691        ORYLA:ENSORLG00000008624            PELSI:ENSPSIG00000010110  PETMA:PETMA04784 | ENSPMAP00000002428 | ENSPMAT00000002440 | ENSPMAG00000002209 | S4RB47_PETMA | ectopic P-granules autophagy protein 5 homolog (C. elegans) [Source:ZFIN;Acc:ZDB-GENE-070705-307]           POEFO:ENSPFOG00000016724            PROCA:ENSPCAG00000009837         SARHA:ENSSHAG00000016721        STRPU:SPU_009882gn           TAEGU:ENSTGUG00000001587            TRICA:TRICA02695 | TCOGS2:TC007876-PA | TCOGS2:TC007876-RA | EFA02217 | TCOGS2:TC007876 | Putative uncharacterized protein GLEAN_07876 [Source:UniProt/SPTREMBL;Acc:D2A2L6]     XENTR:ENSXETG00000032699          XIPMA:ENSXMAG00000007443            ZOONE:ZOONE05703 | KDR20163 | L798_05658 | A0A067RIB6_ZOONE

OMA00286      ANAPL:ENSAPLG00000004580         ANOGA:AGAP001015            FICAL:ENSFALG00000001701           GADMO:ENSGMOG00000016873            GASAC:ENSGACG00000016083       LATCH:ENSLACG00000017995         LOTGI:estExt_Genewise1.C_sca_100441            MACEU:ENSMEUG00000010382         ORENI:ENSONIG00000007454            ORYLA:ENSORLG00000005182        PELSI:ENSPSIG00000010572            POEFO:ENSPFOG00000002502          SARHA:ENSSHAG00000004931        STRPU:SPU_014131gn           TAKRU:ENSTRUG00000018113            TETNG:ENSTNIG00000007203            TRICA:TRICA01407 | TCOGS2:TC004393-PA | TCOGS2:TC004393-RA | CAB65469 | EEZ97204 | TCOGS2:TC004393 | D6X555_TRICA | Putative uncharacterized protein [Source:UniProt/SPTREMBL;Acc:D6X555]            TRISP:TRISP11863 | EFV59892 | EFV59892 | E5S5L0_TRISP     XIPMA:ENSXMAG00000005227

OMA00395      AMPQE:Aqu1.221917 ANAPL:ENSAPLG00000012589         ANOGA:AGAP001234            ASTMX:ENSAMXG00000001395            BRAFL:e_gw.24.103.1           CAEBR:CBG04253      CAPTE:CapteG159536; ELT88015; ELT88015.1         CHICK:ENSGALG00000015465            CIOSA:ENSCSAVG00000007670       DANRE:ENSDARG00000086678         DAPPU:DAPPU19461 | estExt_Genewise1.C_800034 | estExt_Genewise1.C_800034 | E9H7W7_DAPPU | jgi|Dappu1|216243|estExt_Genewise1.C_800034          DROME:FBgn0038344            FICAL:ENSFALG00000005260           GADMO:ENSGMOG00000018158       GASAC:ENSGACG00000014141       HELRO:62279            HUMAN:AAG45474.1; AAH26066.1; AAH50681.1; AAI25212.1; AAI25213.1; BAG37637.1; CAA11679.1; CAC07337.1; CAD39122.1; CAH73862.1; CAI16190.1; CAI19454.1; CAI19627.1; CAI21439.1; EAW48449.1; ENSG00000112249       LEPOC:ENSLOCG00000016550            LOTGI:estExt_Genewise1.C_sca_310097     MELGA:ENSMGAG00000013551        MNELE:ML11543a       MONDO:ENSMODG00000018082            MOUSE:AAH32189.1; AAH59917.1; BAC25644.1; BAC35127.1; ENSMUSG00000038774  MYOLU:MYOLU11526 | ENSMLUP00000002643 | ENSMLUT00000002908 | ENSMLUG00000002886 | G1NYY1_MYOLU | activating signal cointegrator 1 complex subunit 3 [Source:HGNC Symbol;Acc:HGNC:18697]      NEMVE:NEMVE05710 | 88887 | e_gw.19.7.1 | A7RPC5_NEMVE | jgi|Nemve1|88887|e_gw.19.7.1            NOMLE:ENSNLEG00000013890          ONCVO:ONCVO03053 | OVOC11367 | WBGene00248176 | A0A044R7T5_ONCVO            ORENI:ENSONIG00000016540            ORNAN:ENSOANG00000008944        ORYLA:ENSORLG00000004221        POEFO:ENSPFOG00000001462            PROCA:ENSPCAG00000008834         RHOPR:RHOPR11395 | RPRC006785-PA | RPRC006785-RA | RPRC006785 | T1HRW5_RHOPR            SARHA:ENSSHAG00000016496        SORAR:SORAR11709 | ENSSARP00000001765 | ENSSART00000001944 | ENSSARG00000001858 | activating signal cointegrator 1 complex subunit 3 [Source:HGNC Symbol;Acc:18697] STRMM:STRMM09848 | SMAR005190-PA | SMAR005190-RA | SMAR005190 | T1IVJ2_STRMM           STRPU:SPU_017541gn           TAEGU:ENSTGUG00000012262         TAKRU:ENSTRUG00000009819            TETNG:ENSTNIG00000005079            TETUR:TETUR02005 | tetur31g00060.1 | tetur31g00060 | T1L109_TETUR     XIPMA:ENSXMAG00000000071            ZOONE:ZOONE13990 | KDR22605 | L798_12735 | A0A067RPQ7_ZOONE

OMA00419      AEDAE:AAEL011187  AMPQE:Aqu1.226212 ANAPL:ENSAPLG00000004313; EOB00570.1           ANOCA:ENSACAG00000000434            ANOGA:AGAP001519            ASTMX:ENSAMXG00000005684        BRAFL:estExt_fgenesh2_pg.C_1530075       CAEBR:CBG07909            CAEEL:CAB60351.1; Y46G5A.4         CAPTE:CapteG222545; ELU09831; ELU09831.1        CIOIN:ENSCING00000005082            DANRE:ENSDARG00000077536         DAPPU:DAPPU09024 | PASA_GEN_4700063 | PASA_GEN_4700063 | E9GW45_DAPPU | jgi|Dappu1|306253|PASA_GEN_4700063        DASNO:ENSDNOG00000011227        DROME:FBgn0263599 ECHTE:ENSETEG00000000162            FICAL:ENSFALG00000001368           GADMO:ENSGMOG00000004881       GASAC:ENSGACG00000011474       HELRO:102998            HUMAN:AAH07577.1; AAH65924.1; AAS78571.1; BAA34508.2; BAB14906.1; BAC03499.1; CAA94089.1; ENSG00000144028            LATCH:ENSLACG00000000226         LEPOC:ENSLOCG00000015198          LOXAF:ENSLAFG00000015626         MACEU:ENSMEUG00000010532            MELGA:ENSMGAG00000001831        MNELE:ML009128a     MOUSE:AAH63261.1; BAD32303.1; ENSMUSG00000003660            MYOLU:MYOLU13800 | ENSMLUP00000009617 | ENSMLUT00000010552 | ENSMLUG00000010493 | G1PG71_MYOLU | Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:G1PG71]      NASVI:NASVI12725 | NV18250-PA | NV18250-RA | NV18250 | K7JA29_NASVI      NEMVE:NEMVE13119 | 158557 | estExt_gwp.C_40244 | A7RH22_NEMVE | jgi|Nemve1|158557|estExt_gwp.C_40244         NOMLE:ENSNLEG00000000025            ONCVO:ONCVO02166 | OVOC10480 | WBGene00247289 | A0A044QSY4_ONCVO           ORENI:ENSONIG00000010714            ORYLA:ENSORLG00000012286        OTOGA:ENSOGAG00000006879       PELSI:ENSPSIG00000008580  POEFO:ENSPFOG00000015110            PROCA:ENSPCAG00000008536         RHOPR:RHOPR03038 | RPRC004934-PA | RPRC004934-RA | RPRC004934 | T1HLL0_RHOPR            SARHA:ENSSHAG00000000758        SCHMA:SCHMA03051 | Smp_105700__mRNA | CAZ37582 | Smp_105700 | G4LWC6_SCHMA | U520, putative [Source:UniProtKB/TrEMBL;Acc:C4QQ45]      SORAR:SORAR08076 | ENSSARP00000009769 | ENSSART00000010814 | ENSSARG00000010728 | small nuclear ribonucleoprotein 200kDa (U5) [Source:HGNC Symbol;Acc:30859]  STRMM:STRMM13028 | SMAR013162-PA | SMAR013162-RA | SMAR013162 | T1JH32_STRMM          STRPU:SPU_003407gn           TAEGU:ENSTGUG00000014475         TAKRU:ENSTRUG00000001307            TETNG:ENSTNIG00000004320            TRICA:TRICA05851 | TCOGS2:TC016163-PA | TCOGS2:TC016163-RA | EEZ99164 | TCOGS2:TC016163            TRISP:TRISP04502 | EFV51154 | EFV51154 | E5SVP8_TRISP XENTR:ENSXETG00000001243          XIPMA:ENSXMAG00000002058            ZOONE:ZOONE09073 | KDR19736 | L798_05767 | A0A067RJY2_ZOONE

OMA00580      AEDAE:AAEL014733  ANAPL:ENSAPLG00000013269         ASTMX:ENSAMXG00000012552        CHICK:ENSGALG00000003830            DANRE:ENSDARG00000016212         DASNO:ENSDNOG00000016954        ECHTE:ENSETEG00000010224           FICAL:ENSFALG00000001451            GASAC:ENSGACG00000016574       HUMAN:AAH45620.2; AAI05999.1; BAA03515.1; BAD07398.1; CAA45535.1; CAI41111.1; ENSG00000126883            LATCH:ENSLACG00000016871         LOXAF:ENSLAFG00000000807         MACEU:ENSMEUG00000005966         MELGA:ENSMGAG00000005609            MNELE:ML200243a     MOUSE:BAC65471.1; CAM26045.1; ENSMUSG00000001855           MYOLU:MYOLU16674 | ENSMLUP00000004455 | ENSMLUT00000004890 | ENSMLUG00000004875 | G1P3G0_MYOLU | nucleoporin 214kDa [Source:HGNC Symbol;Acc:HGNC:8064]       NASVI:NASVI03100 | NV11673-PA | NV11673-RA | NV11673 | K7IRH5_NASVI     NOMLE:ENSNLEG00000012614          ORENI:ENSONIG00000014974            ORNAN:ENSOANG00000014776        ORYLA:ENSORLG00000006597        OTOGA:ENSOGAG00000016762       PELSI:ENSPSIG00000007417            PIGXX:PIGXX01685 | ENSSSCP00000006118 | ENSSSCT00000006280 | ENSSSCG00000005711 | F1S0W9_PIG | nucleoporin 214kDa [Source:HGNC Symbol;Acc:HGNC:8064]        POEFO:ENSPFOG00000010653          PROCA:ENSPCAG00000009433         SARHA:ENSSHAG00000017178            SORAR:SORAR07461 | ENSSARP00000002707 | ENSSART00000002989 | ENSSARG00000002897 | nucleoporin 214kDa [Source:HGNC Symbol;Acc:8064]       STRPU:SPU_008609gn           TAEGU:ENSTGUG00000004822         TAKRU:ENSTRUG00000007589            TETNG:ENSTNIG00000006197            TRICA:TRICA04870 | TCOGS2:TC014339-PA | TCOGS2:TC014339-RA | EFA04104 | TCOGS2:TC014339            XENTR:ENSXETG00000001475          XIPMA:ENSXMAG00000011331          ZOONE:ZOONE06147 | KDR13700 | L798_12346 | A0A067R682_ZOONE

OMA00689      ANOCA:ENSACAG00000012527       DASNO:ENSDNOG00000005137        LATCH:ENSLACG00000002242            LOTGI:estExt_Genewise1Plus.C_sca_20550            NEMVE:NEMVE00937 | 10482 | gw.77.3.1 | jgi|Nemve1|10482|gw.77.3.1            ORENI:ENSONIG00000007521            PIGXX:PIGXX00494 | ENSSSCP00000022107 | ENSSSCT00000032272 | ENSSSCG00000004503 | I3LDH6_PIG | Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:I3LN89]     POEFO:ENSPFOG00000001476          SCHMA:SCHMA09793 | Smp_149310__mRNA | CAZ32617 | Smp_149310 | Loxhd1, putative [Source:UniProtKB/TrEMBL;Acc:C4QB13]       STRPU:SPU_022482gn           TAEGU:ENSTGUG00000001571            XENTR:ENSXETG00000030605          XIPMA:ENSXMAG00000005112

OMA00713      ANOCA:ENSACAG00000011927       ASTMX:ENSAMXG00000010027        CIOIN:ENSCING00000009459  LATCH:ENSLACG00000012445            LEPOC:ENSLOCG00000004563          MNELE:ML022011a     MONDO:ENSMODG00000001273       MYOLU:MYOLU00062 | ENSMLUP00000009931 | ENSMLUT00000010892 | ENSMLUG00000010877 | G1PGZ8_MYOLU | Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:G1PGZ8]            ONCVO:ONCVO01833 | OVOC10147 | AAA64515 | WBGene00246956 | A0A044QLW3_ONCVO | Paramyosin-like antigen [Source:UniProtKB/TrEMBL;Acc:Q25630]       ORNAN:ENSOANG00000007722        OTOGA:ENSOGAG00000028575       PELSI:ENSPSIG00000010963            SARHA:ENSSHAG00000009967        STRPU:SPU_010054gn

OMA00733      ANAPL:ENSAPLG00000014682; EOA95534.1           ANOCA:ENSACAG00000005340       ASTMX:ENSAMXG00000001859            CHICK:ENSGALG00000013657          CHOHO:ENSCHOG00000004113        DANRE:ENSDARG00000095890         DASNO:ENSDNOG00000012889            ECHTE:ENSETEG00000011718           FICAL:ENSFALG00000004682           GADMO:ENSGMOG00000006668       HUMAN:ENSG00000130856            LATCH:ENSLACG00000010627         LEPOC:ENSLOCG00000003926          MELGA:ENSMGAG00000008045        MONDO:ENSMODG00000012304            MOUSE:ENSMUSG00000041258        MYOLU:MYOLU06368 | ENSMLUP00000010140 | ENSMLUT00000011125 | ENSMLUG00000011089 | G1PHI7_MYOLU | zinc finger protein 236 [Source:HGNC Symbol;Acc:HGNC:13028]            NOMLE:ENSNLEG00000009319            ORENI:ENSONIG00000007298            ORNAN:ENSOANG00000005983        ORYLA:ENSORLG00000020729        OTOGA:ENSOGAG00000027487            PELSI:ENSPSIG00000017900  PETMA:PETMA00625 | ENSPMAP00000005206 | ENSPMAT00000005225 | ENSPMAG00000004710 | S4RJ24_PETMA | zinc finger protein 236 [Source:ZFIN;Acc:ZDB-GENE- 041111-195] PIGXX:PIGXX00866 | ENSSSCP00000019907 | ENSSSCT00000025136 | ENSSSCG00000023533 | I3L7A3_PIG | Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:I3L7A3]  POEFO:ENSPFOG00000019091            PROCA:ENSPCAG00000008132         SARHA:ENSSHAG00000013079        STRPU:SPU_021757gn           TAEGU:ENSTGUG00000009074            XENTR:ENSXETG00000010789

OMA00785      AEDAE:AAEL012462  ANAPL:ENSAPLG00000007548         ANOCA:ENSACAG00000009522       ANOGA:AGAP000314            ASTMX:ENSAMXG00000021135        CAEBR:CBG04404      CAEEL:CAA94301.2; R09E10.7          CAPTE:CapteG164592; ELU02768; ELU02768.1            CHICK:ENSGALG00000005134          CIOIN:ENSCING00000000089  CIOSA:ENSCSAVG00000000412       DANRE:ENSDARG00000069397            DASNO:ENSDNOG00000040336        DROME:FBgn0085430 FICAL:ENSFALG00000007047           GADMO:ENSGMOG00000004298            GASAC:ENSGACG00000002470       HELRO:190028            HUMAN:AAH40726.1; AAH63694.1; AAI11007.1; AAI17206.1; AAI37250.1; AAI37251.1; AAI51207.1; BAA74936.2; BAB14664.1; BAC03709.1; ENSG00000214655   LATCH:ENSLACG00000003591            LEPOC:ENSLOCG00000012853          LOTGI:estExt_Genewise1Plus.C_sca_50305            LOXAF:ENSLAFG00000020554            MELGA:ENSMGAG00000006483        MOUSE:AAH49362.1; AAH59058.1; AAH85161.1; AAI51047.1; AAI51057.1; AAI51174.1; BAB26298.1; BAC26361.1; BAC41457.3; BAE27886.1; ENSMUSG00000021819   MYOLU:MYOLU05929 | ENSMLUP00000022271 | ENSMLUT00000031188 | ENSMLUG00000028244 | G1QEY8_MYOLU | zinc finger, SWIM-type containing 8 [Source:HGNC Symbol;Acc:HGNC:23528]            NOMLE:ENSNLEG00000016744          ONCVO:ONCVO06479 | OVOC4783 | WBGene00241592 | A0A044TH40_ONCVO            ORENI:ENSONIG00000007126            OTOGA:ENSOGAG00000028969       PIGXX:PIGXX05641 | ENSSSCP00000010990 | ENSSSCT00000011282 | ENSSSCG00000010309 | F1SU41_PIG | zinc finger, SWIM-type containing 8 [Source:HGNC Symbol;Acc:HGNC:23528]    POEFO:ENSPFOG00000014225            RHOPR:RHOPR04009 | RPRC010650-PA | RPRC010650-RA | RPRC010650 | T1I2Y1_RHOPR           STRPU:SPU_025573gn            TAEGU:ENSTGUG00000006902         TETNG:ENSTNIG00000005820            TRICA:TRICA01142 | TCOGS2:TC011389-PA | TCOGS2:TC011389-RA | EEZ97539 | TCOGS2:TC011389          TRISP:TRISP12569 | EFV59176 | EFV59176 | E5S7Q8_TRISP XENTR:ENSXETG00000010000            XIPMA:ENSXMAG00000015092

OMA00801      AEDAE:AAEL006809  AMPQE:Aqu1.217330 ANAPL:ENSAPLG00000003120         ANOGA:AGAP003921            ASTMX:ENSAMXG00000002279        BRAFL:fgenesh2_pg.scaffold_29000090      CAEBR:CBG18206      CAEEL:AAS65872.1; ABI94564.1; C27F2.2; CCD65740.1; CCD65747.1   CAPTE:CapteG150573; ELU07210; ELU07210.1        CHICK:ENSGALG00000016868            CHOHO:ENSCHOG00000004372        CIOSA:ENSCSAVG00000009833       DANRE:ENSDARG00000001835         DAPPU:DAPPU04097 | e_gw1.58.55.1 | e_gw1.58.55.1 | E9H0I3_DAPPU | jgi|Dappu1|56737|e_gw1.58.55.1           DASNO:ENSDNOG00000018040            ECHTE:ENSETEG00000008278           FICAL:ENSFALG00000004321           GADMO:ENSGMOG00000019593       HELRO:155980            HUMAN:AAH28390.1; AAH64343.1; AAN10255.1; AAN16023.1; BAD18738.1; CAH73919.1; CAI16648.1; CAI40711.1; EAX09045.1; EAX09050.1; ENSG00000102452     LATCH:ENSLACG00000000937         LEPOC:ENSLOCG00000002812          MACEU:ENSMEUG00000012940            MONDO:ENSMODG00000007346       MOUSE:ENSMUSG00000000197        NASVI:NASVI05784 | NV14975-PA | NV14975-RA | NV14975 | K7J0U4_NASVI           NEMVE:NEMVE06191 | 93026 | e_gw.32.250.1 | A7RTZ8_NEMVE | jgi|Nemve1|93026|e_gw.32.250.1            NOMLE:ENSNLEG00000007834          ONCVO:ONCVO04317 | OVOC8510 | WBGene00245319 | A0A044V3C9_ONCVO            ORENI:ENSONIG00000006795            ORNAN:ENSOANG00000011307        ORYLA:ENSORLG00000011051        OTOGA:ENSOGAG00000011448            PELSI:ENSPSIG00000009830  POEFO:ENSPFOG00000012336          PROCA:ENSPCAG00000014994         SARHA:ENSSHAG00000009122            STRMM:STRMM10656 | SMAR002485-PA | SMAR002485-RA | SMAR002485 | T1INA8_STRMM      STRPU:SPU_027748gn            TAEGU:ENSTGUG00000010876         TAKRU:ENSTRUG00000012145         TETUR:TETUR06558 | tetur15g00870.1 | tetur15g00870 | T1KM99_TETUR            TRICA:TRICA07313 | TCOGS2:TC001338-PA | TCOGS2:TC001338-RA | EEZ98774 | TCOGS2:TC001338 | D6WC81_TRICA           TRISP:TRISP15421 | EFV56251 | EFV56251 | E5SG35_TRISP         XENTR:ENSXETG00000024584          XIPMA:ENSXMAG00000013393          ZOONE:ZOONE13463 | KDR15005 | L798_10696 | A0A067QXN4_ZOONE

OMA00857      AEDAE:AAEL013729  ANAPL:ENSAPLG00000012422         ANOCA:ENSACAG00000006624       CHICK:ENSGALG00000009158            CHOHO:ENSCHOG00000009933        CIOSA:ENSCSAVG00000007013       DANRE:ENSDARG00000104283         DAPPU:DAPPU08883 | e_gw1.24.3.1 | e_gw1.24.3.1 | E9GIN1_DAPPU | jgi|Dappu1|50846|e_gw1.24.3.1    DASNO:ENSDNOG00000011998        DROME:FBgn0023081            FICAL:ENSFALG00000011522           HELRO:191553            HUMAN:AAB37126.1; BAA32296.2; BAD92205.1; CAD57745.1; CAD57746.1; CAH71183.1; CAH71184.1; CAH71185.1; CAH71336.1; CAH71337.1; CAH71338.1; CAI19108.1; CAI19109.1; CAI19110.1; CAI19113.1; CAI46252.1; ENSG00000143776     LOXAF:ENSLAFG00000002527         MONDO:ENSMODG00000006246       MOUSE:ENSMUSG00000026490            MYOLU:MYOLU14906 | ENSMLUP00000006303 | ENSMLUT00000006899 | ENSMLUG00000006863 | G1P829_MYOLU | CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:HGNC:1737]   NOMLE:ENSNLEG00000013980          ONCVO:ONCVO07757 | OVOC6066 | WBGene00242875 | A0A044U2J3_ONCVO            ORENI:ENSONIG00000001238            ORNAN:ENSOANG00000010240        OTOGA:ENSOGAG00000016679            PELSI:ENSPSIG00000017372  PIGXX:PIGXX01926 | ENSSSCP00000011580 | ENSSSCT00000011884 | ENSSSCG00000010862 | F1S8P5_PIG | CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:HGNC:1737]   PROCA:ENSPCAG00000011087         RHOPR:RHOPR06406 | RPRC009486-PA | RPRC009486-RA | RPRC009486 | T1HZL6_RHOPR          SORAR:SORAR12630 | ENSSARP00000001507 | ENSSART00000001661 | ENSSARG00000001616 | CDC42 binding protein kinase alpha (DMPK-like) [Source:HGNC Symbol;Acc:1737]        STRPU:SPU_020069gn            TAEGU:ENSTGUG00000004365         TETUR:TETUR03482 | tetur26g01780.1 | tetur26g01780 | T1KXY2_TETUR    XENTR:ENSXETG00000022112            XIPMA:ENSXMAG00000010796

OMA00938      ANAPL:ENSAPLG00000002878         CAEBR:CBG01265      CAEEL:CCD70457.1; Y39D8C.1          CHICK:ENSGALG00000001967            CIOSA:ENSCSAVG00000008073       DANRE:ENSDARG00000100524         DAPPU:DAPPU18610 | NCBI_GNO_10100001 | NCBI_GNO_10100001 | jgi|Dappu1|328211|NCBI_GNO_10100001       DASNO:ENSDNOG00000041420        FICAL:ENSFALG00000004730           GADMO:ENSGMOG00000004678            GASAC:ENSGACG00000011277       HUMAN:AAC50967.1; AAH20724.1; AAH62779.1; AAI40896.1; AAI46867.1; AAY57325.1; BAB86781.1; CAA65825.1; EAW85515.1; ENSG00000167972       LATCH:ENSLACG00000011593         LEPOC:ENSLOCG00000002542            LOTGI:estExt_fgenesh2_pg.C_sca_80006    LOXAF:ENSLAFG00000000732         MACEU:ENSMEUG00000003597            MONDO:ENSMODG00000015843       MOUSE:AAL99380.1; BAE32771.1; ENSMUSG00000024130            MYOLU:MYOLU13175 | ENSMLUP00000015334 | ENSMLUT00000016826 | ENSMLUG00000016811 | G1PVG9_MYOLU | ATP-binding cassette, sub-family A (ABC1), member 3 [Source:HGNC Symbol;Acc:HGNC:33]            NEMVE:NEMVE01940 | 30195 | gw.10.6.1 | jgi|Nemve1|30195|gw.10.6.1       NOMLE:ENSNLEG00000009302            ORENI:ENSONIG00000005221            ORYLA:ENSORLG00000008142        PIGXX:PIGXX10745 | ENSSSCP00000008599 | ENSSSCT00000008823 | ENSSSCG00000008051 | F1RFA0_PIG | Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:F1RFA0]           POEFO:ENSPFOG00000010081            PROCA:ENSPCAG00000004560         STRMM:STRMM09115 | SMAR000954-PA | SMAR000954-RA | SMAR000954 | T1IJ95_STRMM            STRPU:SPU_023617gn           TAEGU:ENSTGUG00000003346         TAKRU:ENSTRUG00000007310         TETNG:ENSTNIG00000009748            XENTR:ENSXETG00000020232          XIPMA:ENSXMAG00000004756

OMA00967      AEDAE:AAEL009806  ANAPL:ENSAPLG00000012219         ANOCA:ENSACAG00000004466       ANOGA:AGAP011770            ASTMX:ENSAMXG00000000673        BRAFL:estExt_fgenesh2_pg.C_1100061       CAPTE:CapteG160497; ELT98153; ELT98153.1            CHICK:ENSGALG00000011558          CHOHO:ENSCHOG00000001921        DAPPU:DAPPU04587 | NCBI_GNO_0200224 | NCBI_GNO_0200224 | E9FT42_DAPPU | jgi|Dappu1|310287|NCBI_GNO_0200224     DASNO:ENSDNOG00000011984        ECHTE:ENSETEG00000016460            FICAL:ENSFALG00000002607           GADMO:ENSGMOG00000016937       GASAC:ENSGACG00000000598       HUMAN:ENSG00000281324            LATCH:ENSLACG00000018313         LEPOC:ENSLOCG00000016494          LOTGI:fgenesh2_pg.C_sca_123000026            LOXAF:ENSLAFG00000016788         MELGA:ENSMGAG00000013850        MONDO:ENSMODG00000018237       MOUSE:ENSMUSG00000030201            MYOLU:MYOLU02110 | ENSMLUP00000009809 | ENSMLUT00000010760 | ENSMLUG00000010736 | G1PGN5_MYOLU | low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:HGNC:6698]  NASVI:NASVI06099 | NV14309-PA | NV14309-RA | NV14309 | K7IYY2_NASVI            NEMVE:NEMVE13117 | 158520 | estExt_gwp.C_40153 | A7RGY8_NEMVE | jgi|Nemve1|158520|estExt_gwp.C_40153            NOMLE:ENSNLEG00000003488          ORENI:ENSONIG00000007451            ORNAN:ENSOANG00000006877        OTOGA:ENSOGAG00000007729            PELSI:ENSPSIG00000009050  PIGXX:PIGXX13164 | ENSSSCP00000000656 | ENSSSCT00000000671 | ENSSSCG00000000625 | F1SQ65_PIG | low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:HGNC:6698]        POEFO:ENSPFOG00000002186            PROCA:ENSPCAG00000004688         SARHA:ENSSHAG00000013979        SORAR:SORAR09301 | ENSSARP00000005685 | ENSSART00000006269 | ENSSARG00000006249 | low density lipoprotein receptor-related protein 6 [Source:HGNC Symbol;Acc:6698]    STRMM:STRMM07175 | SMAR009116-PA | SMAR009116-RA | SMAR009116 | T1J651_STRMM   STRPU:SPU_023044gn           TAEGU:ENSTGUG00000012717         TAKRU:ENSTRUG00000002629            TETNG:ENSTNIG00000003359            TRICA:TRICA03251 | TCOGS2:TC008151-PA | TCOGS2:TC008151-RA | EFA02463 | TCOGS2:TC008151 | Putative uncharacterized protein GLEAN_08151 [Source:UniProt/SPTREMBL;Acc:D2A038]            XENTR:ENSXETG00000008917            XIPMA:ENSXMAG00000002781          ZOONE:ZOONE01675 | KDR08547 | L798_01759 | A0A067QSV8_ZOONE

 

Appendix 4: Trees constructed in ExaML from SGO family alignments.

OMA00018:

OMA00023:

OMA00048:

 

OMA00194:

OMA00857:

 

 

 

 

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