RetrogeneDB ID: retro_btau_697

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:39423989..39424307(+)
• Located in intron of: ENSBTAG00000002769

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIP5
• Ensembl ID: ENSBTAG00000021805
• Aliases: C13H20orf24, RIP5
• Description: RAB5-interacting protein [Source:RefSeq peptide;Acc:NP_001029593]

Sequence

>retro_btau_697
GTCTGGAGCAAGGTGCTGTGGAGCGACACGGCCTGGGAAGACAAGGATGAATTTTTAGATGTGATCCACTGGTTCTGACA
GATCATTGCTGTGGTCTTAGGTGTCATTTGGGGAGTGTTACCACTGCGAGGTTTCTTGGCAATAGCTGGGTTCTGCCTGA
TCAACGTGGGTGTCGTGTACCTCTACTTCAGCAACTACCTGCAGATGGACGAGGAAGAATATCGCGGCACGTGGGAGCTC
ACAGAAGAAGGGTTTATGACATCGTTTACCTTGTTCATGGTCACCTGGATCATCTTCTACACTGCCATCCACTATGAC

Alignment

ORF - retro_btau_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.79 %
• Parental protein coverage: 82.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VWSKVLRSDAAWEDKDEFLDVIYWFRQIIAVVLGVIWGVLPLRGFLGIAGFCLINAGVLYVYFSNYLQID
          VWSKVL.SD.AWEDKDEFLDVI.WF.QIIAVVLGVIWGVLPLRGFL.IAGFCLIN.GV.Y.YFSNYLQ.D
Retrocopy VWSKVLWSDTAWEDKDEFLDVIHWF*QIIAVVLGVIWGVLPLRGFLAIAGFCLINVGVVYLYFSNYLQMD

Parental  EEEYGGTWELTKEGFMTSFALFMVIWIIFYTAVHYD
          EEEY.GTWELT.EGFMTSF.LFMV.WIIFYTA.HYD
Retrocopy EEEYRGTWELTEEGFMTSFTLFMVTWIIFYTAIHYD

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	0.07 RPM	15.72 RPM
ERP005899_muscle	0.16 RPM	30.09 RPM
SRP017611_brain	0.05 RPM	11.60 RPM
SRP017611_kidney	0.12 RPM	21.99 RPM
SRP017611_liver	0.00 RPM	79.13 RPM
SRP030211_testis	0.05 RPM	11.46 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_697 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_697 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021805	1 retrocopy	retro_btau_697 ,
Cavia porcellus	ENSCPOG00000011435	2 retrocopies	retro_cpor_1090, retro_cpor_1382,
Mustela putorius furo	ENSMPUG00000017777	1 retrocopy	retro_mputfur_1460,
Otolemur garnettii	ENSOGAG00000000891	1 retrocopy	retro_ogar_1796,
Rattus norvegicus	ENSRNOG00000020317	1 retrocopy	retro_rnor_2185,