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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.