RetrogeneDB ID: retro_btau_780

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:6547120..6549406(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000035172
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKRIR
• Ensembl ID: ENSBTAG00000031609
• Aliases: None
• Description: 52 kDa repressor of the inhibitor of the protein kinase [Source:RefSeq peptide;Acc:NP_001179132]

Sequence

>retro_btau_780
ATGCCGAACTTCTGCGCGGCCCCCAACTGCACGCGGAAGAGCACGCAGTCGGACCTGGCCTTCTTCAGGTTCCCGCGGGA
TCCGACCAGATGCCAGAAGTGGGTGGAGAACTGTAGGAGAGCAGACTTAGAAGATAAAACACCTGATCAACTAAATAAAC
ATTATCGATTGTGTGCCAAACACTTTGAAACTTCTATGATCTGCAAAACTAGTCCTTACAGGACAGTTCTCCGAGATAAT
GCCATACCAACAATATTCGATCTTAGCAGCCGTTTGAATAATCCACATAGTAGACACAGAAAACGAATAAAAGAATTGAG
TGAAGATGAAATCAGGACACTGAAACAGAAAAAAATTGATGAAACTTCTGAACAGGAACCAAAACATAAGGAAATAAACA
ACAGCAATGCTCAGAATCCCAGTGCAGAAGAAGTGGGTGAAGAGCAGGATGAAGACATTTTACCTTTAACTCTTGAAGAG
AAGGAAAACAAGGAATATTTAAAATCTTTATTTGAAATTTTGATTCTTATGGGAAAACAAAACATACCTCTGGATGGACA
TGAAACTGATGAAATCCCAGAAGGTCTTTTTACTCCTGATAACTTTCAAGCACTGCTAGAGTGCCGGATCAATTCTGGTG
AAGAGGTTCTGAGAAAGCGCTTTGAGACAACAGCAGTTAACACATTGTTCTGTTCCAAAACACAGCAGAAACAGATGCTG
GAGATCTGTGAGAGCTGCATTCGGGAAGAAACCCTCAGGGAAGTGAGAGATTCTCACTTCTTTTCCATCATCACTGATGA
TGTGGTGGACATAGCAGGGGAAGAGCACCTGCTGGTGTTGGTGAGGTTTGTCGACGAAGCTCATAACCTGAGAGAGGAAT
TTGTAGGCTTCCTGCCTTAACAAGCTGATGCAGAAATTTTGGCTGTGAAATTTCACACTACAATAACTGAGAAATGGGGA
TTAAACATGGAGTACTGTCGTGGCCAGGCTTACATTGTATCTAGTGGATTTTCATCCAAAATGAAAGTTGTTGCTTCTAG
ACTTTTAGAGAAATATCCCCAAGCTATCTACACACTCTGCTCTTCCTGTGCCTTAAATATGTGGTTGGCAAAATCAGTGC
CTGTTATGGGAGTATCTGTTGCATTAGGAACAATTGAGGAAGTTTGTTCTTTTTTTCATCGATCACCACAACTGCTTTTA
GAGCTTGAAAATGTAATTTCTCTCCTCTTTCAGAACAATGAAGAAAGGGGCAAAGAACTGAAGGAAATTTGCCATTCTCA
GTGGACAGGCAGGCATGATGCTTTTGAAATCTTAGTGGACCTCCTACAAGCACTTGTTTTATGTTTAGATGGTATAAATA
GTGACACAAATGTTAGATGGAATAACTGTATAGCTGGCCGAGCATTTGTGCTCTGTAGTGCGGTAACAGATTTTGATTTC
ATCGTTACCATTGTTGTTCTTAAAAATGTTTTATCTTTTACAAGAGCTTTTGGGAAAAATCTTCAGGGGCAAACCTCTGA
TGTCTTTTTTGCAGCCAGTAGCTTGACTGCAGTGTTACATTCACTAAATGAAGTGATGGAAAATATTGAAGTTTATCATG
AATTTTGGTTTGAGGAAGCCACAAATTTGGCAACCAAACTTGATATTCAGATGAAACTCCCAGGGAAATTTCGCAGAGCT
CAGCACAGTAACCTGGAATCTCAGCTAACCTCTGAGAGTTACTACAAAGAGACTCTAAGTGTTCCAACTGTGGAACACAT
TATTCAGGAACTGAAAGATATATTCTCAGAACAGCACCTCAAAGCGCTTAAATGCTTATCCCTGGTACCCTCTGTCATGG
GACAGCTCAAATTCAATACATCAGAGGAGCACCATGCTGACATGTACCGAAGTGACTTACCTAATTCTGACACACTCTCT
GCTGAGCTGCATTGTTGGAGAATTAAATGGAAACACAGAGGGAAAGATATAGAACTTCCATCCACTATTTATGAAGCCCT
TCATCTACCAGACATCAAGTTTTTTCCTAATGTTTATGCATTGCTGAAGGTCCTATGTATTCTTCCTGTGATGAAAGTTG
AGAATGAACGCTATGAAAATGGGCGAAAGCGTCTCAAAGCATACCTGAGGAACACTTTAACAGATCAAAGATCAAGTAAC
TTGGCTTTGCTTAACATAAATTTTGATATAAAACACGATTTGGATTTAATGGTGGATACATATATCAAACTGTATACAAG
TAAGTCAGAGCTTCCTACAGATAATTCAGAAACCATTGAAAATACC

Alignment

ORF - retro_btau_780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNFCAAPNCTRKSTQSDLAFFRFPRDPTRCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRT
          MPNFCAAPNCTRKSTQSDLAFFRFPRDPTRCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMIC.T
Retrocopy MPNFCAAPNCTRKSTQSDLAFFRFPRDPTRCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICKT

Parental  SPYRTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEPKHKEINNSNAQNP
          SPYRTVLRDNAIPTIFDL.S.LNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEPKHKEINNSNAQNP
Retrocopy SPYRTVLRDNAIPTIFDLSSRLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEPKHKEINNSNAQNP

Parental  SAEEVGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHETDEIPEGLFTPDNFQALLECRI
          SAEEVGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHETDEIPEGLFTPDNFQALLECRI
Retrocopy SAEEVGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHETDEIPEGLFTPDNFQALLECRI

Parental  NSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLPVL
          NSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHL.VL
Retrocopy NSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLLVL

Parental  VRFVDEAHNLREEFVGFLPYEADAEILAVKFHTTITEKWGLNMEYCRGQAYVVSSGFSSKMKVVASRLLE
          VRFVDEAHNLREEFVGFLP..ADAEILAVKFHTTITEKWGLNMEYCRGQAY.VSSGFSSKMKVVASRLLE
Retrocopy VRFVDEAHNLREEFVGFLP*QADAEILAVKFHTTITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLE

Parental  KYPQAIYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELENVISLLFQNNEERGKEL
          KYPQAIYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELENVISLLFQNNEERGKEL
Retrocopy KYPQAIYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELENVISLLFQNNEERGKEL

Parental  KEICHSQWTGRHDAFEILVDLLQALVLCLDGINSDTNVRWNNCIAGRAFVLCSAVTDFDFIVTIVVLKNV
          KEICHSQWTGRHDAFEILVDLLQALVLCLDGINSDTNVRWNNCIAGRAFVLCSAVTDFDFIVTIVVLKNV
Retrocopy KEICHSQWTGRHDAFEILVDLLQALVLCLDGINSDTNVRWNNCIAGRAFVLCSAVTDFDFIVTIVVLKNV

Parental  LSFTRAFGKNLQGQTSDVFFAASSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLDIQMKLPGKFRRA
          LSFTRAFGKNLQGQTSDVFFAASSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLDIQMKLPGKFRRA
Retrocopy LSFTRAFGKNLQGQTSDVFFAASSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLDIQMKLPGKFRRA

Parental  QHSNLESQLTSESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTSEEHHADMYR
          QHSNLESQLTSESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTSEEHHADMYR
Retrocopy QHSNLESQLTSESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTSEEHHADMYR

Parental  SDLPNPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCILPVMKVENERYEN
          SDLPN.DTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCILPVMKVENERYEN
Retrocopy SDLPNSDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCILPVMKVENERYEN

Parental  GRKRLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETIENT
          GRKRLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETIENT
Retrocopy GRKRLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETIENT

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	0.22 RPM	5.34 RPM
ERP005899_muscle	0.05 RPM	13.94 RPM
SRP017611_brain	0.00 RPM	6.17 RPM
SRP017611_kidney	0.18 RPM	6.82 RPM
SRP017611_liver	0.23 RPM	4.98 RPM
SRP030211_testis	0.00 RPM	13.16 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_780 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000024488	1 retrocopy	retro_acar_167,
Bos taurus	ENSBTAG00000031609	2 retrocopies	retro_btau_1797, retro_btau_780 ,
Canis familiaris	ENSCAFG00000005274	1 retrocopy	retro_cfam_663,
Equus caballus	ENSECAG00000021982	1 retrocopy	retro_ecab_150,
Homo sapiens	ENSG00000137492	1 retrocopy	retro_hsap_4080,
Mustela putorius furo	ENSMPUG00000008784	1 retrocopy	retro_mputfur_1571,
Pan troglodytes	ENSPTRG00000004091	1 retrocopy	retro_ptro_2766,
Tursiops truncatus	ENSTTRG00000013287	1 retrocopy	retro_ttru_126,