RetrogeneDB ID: retro_btau_1296

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:99695135..99696400(-)
• Located in intron of: ENSBTAG00000015647

Retrocopy information

• Ensembl ID: ENSBTAG00000046570
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSR
• Ensembl ID: ENSBTAG00000007115
• Aliases: None
• Description: glutathione reductase, mitochondrial [Source:RefSeq peptide;Acc:NP_001107662]

Sequence

>retro_btau_1296
GTGAATGTCGGATGTGTACCCAAAAAGGTAATGTGGAACACTGCTGTCCACTCTGAATTCATGCATGACCACGTTGATTA
TGGCTTTCAAAGTTGTGAAAGTAAATTCAATTGGCGGATTATAAAGGAAAAGCGGGATGCCTATGTGAGCCGTCTGAACA
CCATCTATCAAAATAATCTAACCAAATCCCACATAGACATCATCCATGGCCATGCAGCATTCACGTGCGATCCCCAGCCC
ACAGTGGAGGTCAACAGGAGAAAATACACCGCTCCTCACATCCTGATCGCCACAGGCGGCGTGCCCTCGGTTCCTCAGGA
GAGCCAGATCCCCGGTGCCAGCCTAGGAATAACCAGTGATGGGTTTTTTCAGCTGGAAGAGTTGCCTCGCTGCAGTGTCA
TTGTTGGTGCTGGTTACATCGCTGTGGAGATAGCTGGCATCCTGTCTGCCCTGGGTTCTAAGACATCAATAATGATTCGG
CATGATAAGGTGCTTAGAACTCTTGATTCAATAATCAGTTCCAACTGTACCGATGAGCTGGAGAACGCTGGCATTGAGGT
GCTGAAGTACTCCCAGGTCAGGGAAGTTAAAAAAACTTCTTCGGGCCTGGAACTCCGCATGGTTACTTCGATTCCTGGTA
GGGAACCCACCTTCACCACTATTGCAGATGTTGACTGCCTGCTCTGGGCCATTGGGTGGGATCCAAACTCCTGGGGCCTG
AATTTAAACAAACTGGGGGTTCAAACTGATGACAAAGGTCATATCATAGAAGATGAATTCCAGAATACTAACGTAAAAGG
TGTCTATGCAGTTGGGGATGTGTGTGGACATGCTCTTCTTACTCCAGTTGCAATTGCTGCTGGCCGAAAACTTGCCCATA
GACTTTTTGAGTGCAAAGAAGATTCCAAATTAGACTATGACAACATCCCCACAGTGGTCTTCAGCCACCCCCGCCCCCAC
TATTAGGACAGTGGGACTCACAGAAGATGAAGCCATTTATAAATATGGAAAAGAAAATCTGAAGACATTCAACCACCTTT
ACCCCAATGTATCATGCAGTTACCAAAAGGAAAACAAAATGTGTGATGCAAATGGTTTGTGCCAACCAAGAGGAAAAGGT
GGTTGGAATTCATATGCAGGGAATTGGATGTGATGAAATGCTGCAGGGCTTTGCAGTTGCATTGAAAATGGGAGCAACAA
CATCCGACTTTGGTAACATGGTTGCTATTCATCCTACCTCTTCAGAAGAACTGGTCACACTTCGC

Alignment

ORF - retro_btau_1296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNVGCVPKKVMWNTAVHSEFMHDHVDYGFQSCESKFNWRIIKEKRDAYVSRLNTIYQNNLTKSHIDIIHG
          VNVGCVPKKVMWNTAVHSEFMHDHVDYGFQSCESKFNWRIIKEKRDAYVSRLNTIYQNNLTKSHIDIIHG
Retrocopy VNVGCVPKKVMWNTAVHSEFMHDHVDYGFQSCESKFNWRIIKEKRDAYVSRLNTIYQNNLTKSHIDIIHG

Parental  HAAFTCDPQPTVEVNGKKYTAPHILIATGGVPSVPQESQIPGASLGITSDGFFQLEELPRRSVIVGAGYI
          HAAFTCDPQPTVEVN..KYTAPHILIATGGVPSVPQESQIPGASLGITSDGFFQLEELPR.SVIVGAGYI
Retrocopy HAAFTCDPQPTVEVNRRKYTAPHILIATGGVPSVPQESQIPGASLGITSDGFFQLEELPRCSVIVGAGYI

Parental  AVEIAGILSALGSKTSIMIRHDKVLRTFDSIISSNCTEELENAGIEVLKYSQVREVKKTSSGLELRMVTS
          AVEIAGILSALGSKTSIMIRHDKVLRT.DSIISSNCT.ELENAGIEVLKYSQVREVKKTSSGLELRMVTS
Retrocopy AVEIAGILSALGSKTSIMIRHDKVLRTLDSIISSNCTDELENAGIEVLKYSQVREVKKTSSGLELRMVTS

Parental  IPGREPTFTTIADVDCLLWAIGRDPNSWGLNLNKLGIQTDDKGHIIVDEFQNTNVKGVYAVGDVCGKALL
          IPGREPTFTTIADVDCLLWAIG.DPNSWGLNLNKLG.QTDDKGHII.DEFQNTNVKGVYAVGDVCG.ALL
Retrocopy IPGREPTFTTIADVDCLLWAIGWDPNSWGLNLNKLGVQTDDKGHIIEDEFQNTNVKGVYAVGDVCGHALL

Parental  TPVAIAAGRKLAHRLFECKEDSKLDYDNIPTVVFSH-PPIGTVGLTEDEAIYKY--GKENVKTYSTTFTP
          TPVAIAAGRKLAHRLFECKEDSKLDYDNIPTVVFSH.PP....G....................STTFTP
Retrocopy TPVAIAAGRKLAHRLFECKEDSKLDYDNIPTVVFSH<PPPPLLGQWDSQKMKPFINMEKKI*RHSTTFTP

Parental  MYHAVTKRKTKCVMKMVCANKEEKVVGIHMQGIGCDEMLQGFAVAVKMGATKSDFDNTVAIHPTSSEELV
          MYHAVTKRKTKCVM.MVCAN.EEKVVGIHMQGIGCDEMLQGFAVA.KMGAT.SDF.N.VAIHPTSSEELV
Retrocopy MYHAVTKRKTKCVMQMVCANQEEKVVGIHMQGIGCDEMLQGFAVALKMGATTSDFGNMVAIHPTSSEELV

Parental  TLR
          TLR
Retrocopy TLR

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	41.89 RPM
ERP005899_muscle	0.63 RPM	28.82 RPM
SRP017611_brain	0.46 RPM	9.18 RPM
SRP017611_kidney	1.13 RPM	22.88 RPM
SRP017611_liver	1.13 RPM	26.05 RPM
SRP030211_testis	0.69 RPM	16.25 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1296 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1296 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007115	1 retrocopy	retro_btau_1296 ,
Choloepus hoffmanni	ENSCHOG00000009523	1 retrocopy	retro_chof_2437,
Monodelphis domestica	ENSMODG00000019004	1 retrocopy	retro_mdom_1042,