Skip to main content

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.
Back to article page

Genome Biology

ISSN: 1474-760X

Contact us