RetrogeneDB ID: retro_btau_358

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:99351182..99352541(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000002900
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDIA6
• Ensembl ID: ENSBTAG00000001928
• Aliases: None
• Description: protein disulfide-isomerase A6 precursor [Source:RefSeq peptide;Acc:NP_001193274]

Sequence

>retro_btau_358
AGGCGGCGGCTGGAGTGTGTGGCGGCGCGGGCGCTCAGCATGGCTCGCCTGGTGCTTGGTCTGATGAGCTGTACCCTCTT
TATAACAGTTAATCGTCTGTATTCGTCTAGTGATGATGTAATTGAATTAACCCCCTCAAACTTCAACCGAGAAGTTATTC
AGAGTTACAGTTTGTGGCTTGTAGAATTCTATGCTCCATGGTGTGGCCACTGCCAGAGGTTAACACCAGAATGGAAGAAA
GCAGCAACTGCCTTGAAAGATGTTGTCAAAGTTGGTGCAGTTGACGCAGACAAACATCAGTCCCTAGGGGGTCAGCATGG
TGTTCAGGGATTTCCTACCATTAAGATTTTTGGATCCAACAAAAACAAACCAGAAGATTATCAGGGTGGCGGAACTGGTG
AAGCCATCGTGGACGCTGCCCTCAGTGCTCTGTGCCAGCTTGTGAAAGAACGCCTTGGCGGCCGGGGCAGAGGCTACAGC
TCTGGAAAACAAGGCAGAGGTGACAGTTCAAGTAAGAAGGACGTGATTGAGCTGACGGACGACAACTTTGACAAGAATGT
CCTTGACAGTGAAGATGTTTGGATGGTTGAGTTTTATGCTCCCTGGTGTGGACACTGCAAAAACCTAGAGCCAGAATGGG
CCGCGGCCGCTACAGAGGTGAAAGAGCAAACGAAAGGCAAAGTGAAACTCGCAGCTGTGGATGCCAGTGTGAACCAGGTT
CTCGCCAGCAGATACGGGATTAGGGGATTCCCTACAATCAAGATATTTCAGAAAGGTGAGTCTCCTGTGGATTACGACGG
GGGACGCAGGAGATCCGACATTGTTTCCCGGGCCCTCGATCTGTTTTCTGATAATGCTCCACCTCCTGAGCTGCTTGAGA
TCATCAACGAGGACGTCGCCAAGAAGACGTGTGAGGAGCATCAGCTCTGTGTCGTGGCCGTGGTGCCCCACATTCTTGAC
ACAGGAGCTGCAGGCAGAAATTCTTACTTGGAAGTTCTTCTGAAGTTGGCGGACAAATACAAGAAGAAAATGTGGGGGTG
GCTGTGGACAGAAGCTGGAGCCCAATCTGAACCTGAGAACACGCTGGGGATTGGAGAGTTTGGATACCCTGCTATGGCAG
CTATTAACGCACGCGAGATGAAATTTGCTCTCCTAAAGGGATCGTTCAGTGAGCAAGGCATTAATGAGTTTCTCAGGGAG
CTGTCTTTTGGGCGTGGATCTACGGCGCCTGTAGGCGGTGGTGCTTTCCCCACCATCAGCACCAGGGAGCCCTGGGATGG
CAAGGACGGCGAACTTCCCGTGGAAGATGACATTGACCTGAGTGACGTGGAGCTGGACGACCTGGAGAAAGGTGAATTG

Alignment

ORF - retro_btau_358 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRRLECVAARALSMARLVLGLMSCTLFITVNGLYSSSDDVIELTPSNFNREVIQSDSLWLVEFYAPWCGH
          RRRLECVAARALSMARLVLGLMSCTLFITVN.LYSSSDDVIELTPSNFNREVIQS.SLWLVEFYAPWCGH
Retrocopy RRRLECVAARALSMARLVLGLMSCTLFITVNRLYSSSDDVIELTPSNFNREVIQSYSLWLVEFYAPWCGH

Parental  CQRLTPEWKKAATALKDVVKVGAVDADKHQSLGGQYGVQGFPTIKIFGSNKNKPEDYQGGRTGEAIVDAA
          CQRLTPEWKKAATALKDVVKVGAVDADKHQSLGGQ.GVQGFPTIKIFGSNKNKPEDYQGG.TGEAIVDAA
Retrocopy CQRLTPEWKKAATALKDVVKVGAVDADKHQSLGGQHGVQGFPTIKIFGSNKNKPEDYQGGGTGEAIVDAA

Parental  LSALRQLVKDRLGGRGSGYSSGKQGRGDSSSKKDVIELTDDNFDKNVLDSEDVWMVEFYAPWCGHCKNLE
          LSAL.QLVK.RLGGRG.GYSSGKQGRGDSSSKKDVIELTDDNFDKNVLDSEDVWMVEFYAPWCGHCKNLE
Retrocopy LSALCQLVKERLGGRGRGYSSGKQGRGDSSSKKDVIELTDDNFDKNVLDSEDVWMVEFYAPWCGHCKNLE

Parental  PEWAAAATEVKEQTKGKVKLAAVDATVNQVLASRYGIRGFPTIKIFQKGESPVDYDGGRTRSDIVSRALD
          PEWAAAATEVKEQTKGKVKLAAVDA.VNQVLASRYGIRGFPTIKIFQKGESPVDYDGGR.RSDIVSRALD
Retrocopy PEWAAAATEVKEQTKGKVKLAAVDASVNQVLASRYGIRGFPTIKIFQKGESPVDYDGGRRRSDIVSRALD

Parental  LFSDNAPPPELLEIINEDVAKKTCEEHQLCVVAVLPHILDTGAAGRNSYLEVLLKLADKYKKKMWGWLWT
          LFSDNAPPPELLEIINEDVAKKTCEEHQLCVVAV.PHILDTGAAGRNSYLEVLLKLADKYKKKMWGWLWT
Retrocopy LFSDNAPPPELLEIINEDVAKKTCEEHQLCVVAVVPHILDTGAAGRNSYLEVLLKLADKYKKKMWGWLWT

Parental  EAGAQSELENALGIGGFGYPAMAAINARKMKFALLKGSFSEQGINEFLRELSFGRGSTAPVGGGAFPTIS
          EAGAQSE.EN.LGIG.FGYPAMAAINAR.MKFALLKGSFSEQGINEFLRELSFGRGSTAPVGGGAFPTIS
Retrocopy EAGAQSEPENTLGIGEFGYPAMAAINAREMKFALLKGSFSEQGINEFLRELSFGRGSTAPVGGGAFPTIS

Parental  TREPWDGKDGELPVEDDIDLSDVELDDLEKDEL
          TREPWDGKDGELPVEDDIDLSDVELDDLEK.EL
Retrocopy TREPWDGKDGELPVEDDIDLSDVELDDLEKGEL

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	158.68 RPM
ERP005899_muscle	0.48 RPM	256.61 RPM
SRP017611_brain	0.23 RPM	82.68 RPM
SRP017611_kidney	0.53 RPM	175.62 RPM
SRP017611_liver	1.51 RPM	503.94 RPM
SRP030211_testis	0.93 RPM	237.88 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_358 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_358 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001928	1 retrocopy	retro_btau_358 ,
Bos taurus	ENSBTAG00000008390	1 retrocopy	retro_btau_1105,
Loxodonta africana	ENSLAFG00000012281	1 retrocopy	retro_lafr_820,
Tarsius syrichta	ENSTSYG00000013891	1 retrocopy	retro_tsyr_1661,