RetrogeneDB ID: retro_btau_316

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:137080052..137080423(-)
• Located in intron of: ENSBTAG00000017659

Retrocopy information

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

Parental gene information

• Parental gene symbol: C28H10orf57
• Ensembl ID: ENSBTAG00000001656
• Aliases: TMEM254, C10orf57, C28H10orf57
• Description: Transmembrane protein C10orf57 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q0D2G3]

Sequence

>retro_btau_316
ATGGGGAAGTCGAGAGGAGATGAGGCCTACTTCCAGAGGAGCCATCTGTTCTGGGTTACTGTCATCATCCTTTCTTTTGG
CTATTACACGTGGATGGTCTTCTGGCCTGAGAGTACTCCTTATCAGAGCCTGGGACCCCTGGGCCCTTCACTCAGTACTC
GCTGAAGCATCATCACACCCTCGTGCATGGTTGGTGTTGGCTTGCCTGGATGATTCTCGTGGGAGTGTCCTTGTATGCCA
TTGTATCGCGCAAGTCTAAAGGCATCACGAATACGTGGACCCAACTGCTCTGGTTCCTACAGACGTTCCTTTTCGGGATG
GCATCTCTCTATTACTTGATTGCTTTTAGACCAAAATGCCAAAAACAAACT

Alignment

ORF - retro_btau_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKARGDEAYFQRSSLFWVTIIILSFGYYTWVIFWPESIPYQSLGPLGP-FTQYLLKHHHTLVHAWYWLA
          MGK.RGDEAYFQRS.LFWVT.IILSFGYYTW..FWPES.PYQSLGPLGP.FTQY.LKHHHTLVH.W.WLA
Retrocopy MGKSRGDEAYFQRSHLFWVTVIILSFGYYTWMVFWPESTPYQSLGPLGP<FTQYSLKHHHTLVHGWCWLA

Parental  WMIHVGESLYAIVLCKSKGITNTWTQLLWFLQTFLFGLASLYYLIAFRPKHQKQT
          WMI.VG.SLYAIV..KSKGITNTWTQLLWFLQTFLFG.ASLYYLIAFRPK.QKQT
Retrocopy WMILVGVSLYAIVSRKSKGITNTWTQLLWFLQTFLFGMASLYYLIAFRPKCQKQT

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	66.47 RPM
ERP005899_muscle	0.00 RPM	5.75 RPM
SRP017611_brain	0.00 RPM	26.49 RPM
SRP017611_kidney	0.00 RPM	30.76 RPM
SRP017611_liver	0.00 RPM	19.86 RPM
SRP030211_testis	0.00 RPM	43.62 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_316 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_316 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012986	4 retrocopies	retro_amel_1410, retro_amel_1554, retro_amel_1777, retro_amel_821,
Bos taurus	ENSBTAG00000001656	1 retrocopy	retro_btau_316 ,
Homo sapiens	ENSG00000133678	1 retrocopy	retro_hsap_1692,
Mustela putorius furo	ENSMPUG00000003613	2 retrocopies	retro_mputfur_400, retro_mputfur_407,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Nomascus leucogenys	ENSNLEG00000010657	1 retrocopy	retro_nleu_1337,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Pongo abelii	ENSPPYG00000002293	1 retrocopy	retro_pabe_1393,