RetrogeneDB ID: retro_btau_675

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:37982386..37982938(-)
• Located in intron of: ENSBTAG00000047595

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.49010
• Ensembl ID: ENSBTAG00000001212
• Aliases: None
• Description: translocon-associated protein subunit beta precursor [Source:RefSeq peptide;Acc:NP_001015533]

Sequence

>retro_btau_675
CTGAGGCTGCTGGAGTTTGTGGTGTTCATTCTATTTGCCGTCACACAAGCAGACAAAGTAGCCAGGCTTTGGCCTCAAAA
TCACTGTTGAACAGATGTGCTGTGAAAGGGGAGACCTGATCTTTCAGAACAATATCTACAGTATTGGCTCAAGTGCTACA
TGAGACGTGGACTTGCCTGATGATTCCTTCCTTCCAGAAGACTTCAGCATTGTCTTGGGAATAATCAACATTAAATGGGA
CTGGGTTACTCCTGCTAACAATGTCTCTCACATCATGGCCCTACATCCTCTCAAGGCTGGTTATTTCAGCTTCACCTCAG
CAACTATTCCTTACCTGGCTCAAGAGGATAGGCCCATAGTGATGGACTTTACCAGTGCACCTGAATGGGGAGGAATCCTG
GCTCAGCATAGTTGAATTGTAGATTTTTCCCCCATTTTTTCCTGGACTGCGTAGCTTTCCGGGTTATGACTCTCCCTTCA
ATGGACATCCACCTGCAGTCATGATACTCCAGCAAGAGGAAATATGACATCCCCCAAACCAAAAAAATAACT

Alignment

ORF - retro_btau_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.83 %
• Parental protein coverage: 86.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRLLAFAVLALFAVTQAEEGARL-LASKSLLNRYAVEGR-DLTLQYNIYNVGSSAALDVELSDDSFPPED
          .RLL.F.V..LFAVTQA...ARL.LASKSLLNR.AV.G..DL..Q.NIY..GSSA..DV.L.DDSF.PED
Retrocopy LRLLEFVVFILFAVTQADKVARL<LASKSLLNRCAVKGE<DLIFQNNIYSIGSSAT*DVDLPDDSFLPED

Parental  FGIVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATVTYLAQEDGPVVIGFTSAPGQGGILAQRE
          F.IV.G..N.KWD...PA.NVSH...L.PLKAGYF.FTSAT..YLAQED.P.V..FTSAP..GGILAQ..
Retrocopy FSIVLGIINIKWDWVTPANNVSHIMALHPLKAGYFSFTSATIPYLAQEDRPIVMDFTSAPEWGGILAQHS

Parental  -FDRRFSPH-FLDWAAFGVMTLPSIGVPLLLWYSSKRKYDTPKTKRLS
          ....RF.PH.FLD..AF.VMTLPS....L...YSSKRKYD.P.TK...
Retrocopy <LNCRFFPHFFLDCVAFRVMTLPSMDIHLQS*YSSKRKYDIPQTKKIT

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	85.87 RPM
ERP005899_muscle	0.00 RPM	336.37 RPM
SRP017611_brain	0.00 RPM	66.28 RPM
SRP017611_kidney	0.00 RPM	112.44 RPM
SRP017611_liver	0.00 RPM	219.20 RPM
SRP030211_testis	0.06 RPM	55.10 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_675 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_675 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001212	2 retrocopies	retro_btau_1165, retro_btau_675 ,
Cavia porcellus	ENSCPOG00000023729	1 retrocopy	retro_cpor_478,
Nomascus leucogenys	ENSNLEG00000012304	1 retrocopy	retro_nleu_3102,
Ictidomys tridecemlineatus	ENSSTOG00000028971	1 retrocopy	retro_itri_1381,