Skip to main content

Table 1 Novel genes exclusive to songbirds

From: Comparative genomics reveals molecular features unique to the songbird lineage

Gene name¥

Phylogeny

Ensembl ID

Gene location

SD site

Brain-derived ESTs

Non-brain ESTs

Non-brain RNA-SEQ

A4GALT-related*

      

A4GALT-1

SONGBIRDS†

ENSTGUG00000012139

chr1A:65,194,903-65,195,964

YES

No

No

None

A4GALT-2

SONGBIRDS†

ENSTGUG00000018227

chr1A:65,202,780-65,203,835

YES

No

No

None

A4GALT-3

SONGBIRDS†

ENSTGUG00000018451

chr1A:65,210,658-65,211,719

YES

No

No

None

CASC1-related

     

CASC1-1

SONGBIRDS†

ENSTGUG00000012133

chr1A:65,157,078-65,159,677

FE723736√, DV948439

JV165872, JV165873

Embryo, spleen, testes

CASC1-2

SONGBIRDS†

ENSTGUG00000012243

chr1A:66,373,778-66,384,478

YES

DV948439

JV184784, JV165872, JV165873

Embryo, liver, muscle, testes

FN3KRP-related

      

FN3KRP

ALL BIRDS‡

ENSTGUG00000007633

chr18:6,574624-6,580,544

DV959265√

No

Embryo

FN3KRPL1

SONGBIRDS

No model

chrZ:24,858,422-24,862,943

No

No

Embryo, liver, skin

FN3KRPL2

PASSERINES

ENSTGUG00000006787

chrZ:69,583,022-69,590,574

YES

DV955139√, FE727948√, DV955139√

JV168705√, JV168706√, JR864904√

Embryo, liver, spleen, testes

HYDIN-related*

     

HYDIN

ALL BIRDS‡

No model

chr11:5,451,491-5,475,997

No

No

Liver, muscle, skin, spleen

HYDINL1

SONGBIRDS

ENSTGUG00000009150

chr11:16,377,691-16,404,553

No

JV172391

Muscle, skin, spleen

HYDINL2

PASSERINES

No model

chr11:16,633,304-16,663,944

YES

No

No

Liver, muscle, testes

HYDINL3

ZEBRA FINCH

ENSTGUG00000009256

chr11:17,005,696-17,033,616

YES

No

No

Muscle, testes

HYDINL4

ZEBRA FINCH

No model

chr11:18,229,584-18,238,051

YES

No

No

None

HYDINL5

ZEBRA FINCH

ENSTGUG00000009737

chr11:19,907,326-19,914,490

No

JV172391

Testes

NOVEL (TMRA)

      

TMRA

SONGBIRDS

ENSTGUG00000012248

chr1A:66,486,182-66,494,397

YES

CK302958√

JV159445√, JV159451√

Embryo, liver, muscle, spleen, testes

RIOK2-related

     

RIOK2

ALL BIRDS‡

ENSTGUG00000001223

chrZ:24,872,816-24,883,105

DV956882√

JV172474√, JR863880√

Embryo, liver, muscle, skin, spleen, testes

RIOK2L

SONGBIRDS

No model

chrZ:69,578,247-69,578,886

YES

No

No

Skin

RNF4-related*

     

RNF4

ALL BIRDS‡

ENSTGUG00000010518

chr4:62,477,216-62,484,738

DV951366√

JV183872√, JR867734√

Liver, skin, testes

RNF4L1

SONGBIRDS

No model

chr4:8,201,210-8,201,765

No

No

None

RNF4L2

PASSERINES

ENSTGUG00000018516

chr4:20,660,938-20,751,958

No

No

None

RNF4L3

PASSERINES

ENSTGUG00000018370

chr4:22,411,072-22,433,579

No

No

Embryo, muscle, skin, spleen

RNF4L4

ZEBRA FINCH

ENSTGUG00000018547

chr4:22,445,102-22,478,943

No

No

Testes

RNF4L5

ZEBRA FINCH

ENSTGUG00000018338

chr4:22,507,187-22,517,977

No

No

Muscle, spleen

RNF4L6

ZEBRA FINCH

ENSTGUG00000018226

chr4:22,538,729-22,547,838

No

No

None

RNF4L7

PASSERINES

No model

chr4:41,650,214-41,650,348

No

No

None

URB1-related

     

URB1

ALL BIRDS‡

ENSTGUG00000013442/ no model

chr1:97,555,543-97,592,096/ chr1_random:362,665-365,267

YES

FE722167√

No

Embryo, liver, muscle, skin, testes

URB1L1

ZEBRA FINCH

ENSTGUG00000011753

chr1A:60,924,812-60,941,816

YES

CK301434, CK303889, DV957700

No

Embryo, liver

URB1L2

ZEBRA FINCH

No model

chr1A:63,520,638-63,528,208

CK301434, CK303889

No

None

URB1L3

SONGBIRDS

No model

chr5:4,764,796-4,772,823

YES

CK301434, CK303889, DV957700

No

Skin

URB1L4

ZEBRA FINCH

No model

chr7:1,064,071-1,065,024

No

No

None

URB1L5

ZEBRA FINCH

No model

chr23:2,319,460-2,335,606

YES

DV957700

No

Liver, muscle, spleen, testes

YTHDC2-related*

      

YTHDC2

ALL BIRDS‡

No model

chrZ:21,509,497-21,511,474

YES

No

No

None

YTHDC2L1

SONGBIRDS

ENSTGUG00000014232

chr2_random:378,730-383,125

CK309358√

No

None

YTHDC2L2

ZEBRA FINCH

ENSTGUG00000014992

chr3_random:766,156-785,803

No

No

None

YTHDC2L3

PASSERINES

ENSTGUG00000000643

chrZ:10,792,293-10,809,782

YES

No

JV174477, JV177272

Embyro, liver, muscle, spleen

YTHDC2L4

ZEBRA FINCH

No model

chrZ:29,309,810-29,332,222

No

No

Embryo, liver, muscle, skin, spleen, testes

YTHDC2L5

ZEBRA FINCH

ENSTGUG00000003755

chrZ:55,988,800-56,020,229

DV947064√

JV174477√

Embryo, liver, muscle, skin, spleen, testes

YTHDC2L6

ZEBRA FINCH

ENSTGUG00000004173

chrZ:57,443,052-57,444,728

YES

No

No

Embryo

  1. Families of genes where at least one member has been determined to be present uniquely in all songbirds. Tandem duplicates, where clear orthology cannot be determined, are distinguished with dashed numbers (e.g., CASC-1, CASC-2). Other duplicates are named after being ‘like’ their orthologous parent gene (e.g. RIOK2L). Ensembl IDs and chromosomal locations refer to the Zebra finch genome. Expressed sequence tags (ESTs) providing evidence of gene expression in the brain [57, 81, 82] and RNA-seq data derived from other tissues [27] are from Zebra finch, non-brain ESTs are derived from Dark-eyed junco [37]. ¥: Gene symbols have been corrected based on our curation of Ensembl annotation, *: Gene family previously reported as being expanded in Zebra finch, ‡: Parent gene, †: Parent gene cannot be determined, √: EST is specific to this gene locus.