RetrogeneDB ID: retro_btau_1261

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:23409732..23410046(-)
• Located in intron of: ENSBTAG00000007909

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BT.38237
• Ensembl ID: ENSBTAG00000003997
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 D4 [Source:RefSeq peptide;Acc:NP_001069007]

Sequence

>retro_btau_1261
CCTAATGGCAGCCTGCATCAAGGCAGTATTTTTGTGTGTGTTTTGAAAATTTATATTCCTACAGATTCCACCTTCAAACC
ACCTAAAGTTGCATTTACAAGAATTTATCATCCAAATATTAACAGTAATAGCAGCATATGTATTGATATTCTAAGATCAC
AATGTCCTCCTGCTTCAACTGTTTCTGAAGTTCTTTTTTTATCCATTGGTTCAATGCTATGTCTTCCAAACCCAGATAAC
TCCCGAGTGCCAGGGACTGCACAAATCTATAAAATGACAGAGATAAATACAAGAGTGACCTCAGGAATCTCTGG

Alignment

ORF - retro_btau_1261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.62 %
• Parental protein coverage: 68.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNDSPYQGGVFF--LTIHFPTDYPFKPPKVVFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVL-LSI
          PN.S..QG..F...L.I..PTD..FKPPKV.F.T.IYHPNINSN.SIC.DILRSQ..PA.TVS.VL.LSI
Retrocopy PNGSLHQGSIFVCVLKIYIPTDSTFKPPKVAF-TRIYHPNINSNSSICIDILRSQCPPASTVSEVLFLSI

Parental  CSLLCDPNPDDPLVPEIAHTYKA-DREKYVSSLDCLW
          .S.LC.PNPD...VP..A..YK..DR.KY.S.L..LW
Retrocopy GSMLCLPNPDNSRVPGTAQIYKM<DRDKYKSDLRNLW

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	11.68 RPM
ERP005899_muscle	0.11 RPM	16.63 RPM
SRP017611_brain	0.00 RPM	23.43 RPM
SRP017611_kidney	0.06 RPM	20.03 RPM
SRP017611_liver	0.00 RPM	15.03 RPM
SRP030211_testis	0.03 RPM	89.63 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1261 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1261 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_859

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261 ,
Bos taurus	ENSBTAG00000004161	6 retrocopies	retro_btau_1421, retro_btau_1602, retro_btau_1739, retro_btau_1775, retro_btau_1851, retro_btau_1852,
Bos taurus	ENSBTAG00000020796	5 retrocopies	retro_btau_1174, retro_btau_1314, retro_btau_1773, retro_btau_1774, retro_btau_752,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838, retro_tsyr_919,