RetrogeneDB ID: retro_btau_1472

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:106521638..106521911(+)
• Located in intron of: ENSBTAG00000005711

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1ORF130
• Ensembl ID: ENSBTAG00000012604
• Aliases: None
• Description: None

Sequence

>retro_btau_1472
ACCTCATTCCCACGGACCATGACCCCTAGGGGAGAAGACTTTGTGTACGAGACTTCTGGAGCCATTGCTGCTGCCATCGT
GGTGGCCTGTCATCATCGCCACTGAGGTTCTGATCCTGCCGAAGAGGTATAGCAGGACAACGAGGGCGAGACGGGAGATG
GAGGCCCTGGGCCCCGAGCCAGCCGCCCCTCCTGCCCTGGGCCCAAAAAGCCACAGCAGCCGGCACCCACTGCTGCAACC
CTGAGCCCTGCAGACATCCAGGTGGGGACTCGG

Alignment

ORF - retro_btau_1472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.45 %
• Parental protein coverage: 90.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TIFSLNMTTRGEDFLYKSSGAIIAAVVVI-VIIIFTVVLILLKMYNRKMRTRRELEPKGPKPASPSALGA
          T.F...MT.RGEDF.Y..SGAI.AA.VV..VII..T.VLIL.K.Y.R..R.RRE.E..GP.PA.P.ALG.
Retrocopy TSFPRTMTPRGEDFVYETSGAIAAAIVVA>VIIA-TEVLILPKRYSRTTRARREMEALGPEPAAPPALGP

Parental  NSNSSQQ-PATVTFSPVDIHVETR
          .S.SS...P...T.SP.DI.V.TR
Retrocopy KSHSSRH<PTAATLSPADIQVGTR

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	0.00 RPM
ERP005899_muscle	0.00 RPM	0.32 RPM
SRP017611_brain	0.00 RPM	1.42 RPM
SRP017611_kidney	0.00 RPM	0.24 RPM
SRP017611_liver	0.00 RPM	1.13 RPM
SRP030211_testis	0.09 RPM	0.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1472 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012604	1 retrocopy	retro_btau_1472 ,
Echinops telfairi	ENSETEG00000006813	1 retrocopy	retro_etel_1744,