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Table 2 The genes of the W chromosome

From: Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds

Gene_ID canary Symbols Description (automated assignment) Scaffold ID Zebra finch paralogs Medium ground finch paralogs Canary paralogs Chicken paralogs
SCA_g3451(mRNA) NIPBL Nipped-B-like protein SCA1_u120 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g3507(mRNA) F1P4V8_CHICK Valosin-containing protein [Source:RefSeq peptide;Acc:NP_001038129] SCA1_u125 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g3994(mRNA) - Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:G1MSQ9] SCA1_u139 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g4302(mRNA SMAD2 SMAD family member 2 [Source:HGNC Symbol;Acc:6768] SCAI_uI41 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g4352(mRNA) RASA1 RAS p21 protein activator 1 [Source:HGNC Symbol;Acc:9871] SCAI_u146 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g4788(ab initio)   PREDICTED: zinc finger SWIM domain-containing protein 6 [Gallus gallus] SCA1 u157 No hits! No hits! 1 (putative W) 2 (chrZ/chrW)
SCA_g5540(homology) C18orf25 Uncharacterized protein C18orf25 SCA1u17O 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW, chrUN)
SCA_g5588(mRNA) UBAP2 Ubiquitin associated protein 2 [Source:HGNC Symbol;Acc:14185] SCAI_u177 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g6069(homology) KCMF1 E3 ubiquitin-protein ligase KCMF1 (EC 6.3.2.-) SCAI_u186 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g8416(mRNA) SPINZ_CHICK Spindlin-Z [Source:UniProtKB/Swiss-Prot;Acc:Q90WG1] SCAI_u248 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g8529(homology) F1NGA2_CHICK ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit [Source:RefSeq peptide;Acc:NP_989617] SCAI_u252 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 2 (chrZ/chrW)
SCA_g8946(mRNA) TMED7 CGI-109 Transmembrane emp24 domain-containing protein 7 SCAI_i272 1 (chrZ) 2 (no asgmts) 2 (putative Z/W) 1 (chrZ)
SCA_g5568(mRNA) SMAD4 SMAD family member 4 SCAI_u174 1 (chrUN) 2 (no asgmts) 2 (putative Z/W) 2 (chrUN/chr25)
SCA_g5589(mRNA) - Predicted: proto-oncogene c-Rel-like [Meleagris gallopavo] SCA1_u177 Many Many Many Many, best hit W
SCA_g5590(homology) - Predicted: hypothetical protein [Taeniopygia guttata] SCAI_u177 Many Many Many Many
SCA_g8399(homology) D7F039_TAEGU Fem1c-Z [Source:RefSeq peptide;Acc:NP_001177271] SCAI_u243 1 (chrZ) 2 (no asgmts) 1 (putative W) 1 (chrZ)
SCA_g8945(ab initio) - Fem1c-Z [Taeniopygia guttata] SCA1u272 1 (chrZ) 2 (no asgmts) 1 (putative W) 1 (chrZ)
SCA_g15017(homology) - Uncharacterized protein SCAI_u533 1 (chrUN) 1 (no asgmts) 1 (putative W) 1 (chrW)
  1. The assembled canary W chromosome superscaffolds add up to 1.69 Mbp and thus far contain 12 genes (chicken has 21 genes and 5 RNA genes [49], of which three genes (TMED7, F1P4V8_Chick, and FEM1C_Z) are Z linked in the chicken genome). The assignment of these genes to the W chromosome is supported by the findings that (i) most of these genes have only one paralog in the zebra finch genome assembly, which is lacking the W chromosome, and (ii) one ortholog and one paralog are found on chrZ/chrW of the canary, the chicken and the medium ground finch. In these species, the W chromosome was included in genomic sequencing, although no scaffolds were assigned to chromosomes in the case of the medium ground finch. No asgmts = no assignments.
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