RetrogeneDB ID: retro_btau_636

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:6155905..6156793(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GRHPR
• Ensembl ID: ENSBTAG00000019299
• Aliases: None
• Description: glyoxylate reductase/hydroxypyruvate reductase [Source:RefSeq peptide;Acc:NP_001178966]

Sequence

>retro_btau_636
CAGTGGGATTCTGATGAGCCCATCCCCAGAGAGGACCTGGAACAGAGAATGGCTGGGGCCCAGGGCCTGCTCTGCCTCCT
CTCGGACCGCATAGACAAGAAGCTCCTGGACGCTGCAGGAGCTAATCTCAAAGTCATTAGCACAATGTCTGTAGGTGTCG
ACCACTTGGCTTTGGATGAAATCAAGAAGCGTGGGATCCGTGTGGGCTACACTCCGGGTGTCCTGACAGACGCCACCGCC
GAGCTCGCCGTCTCCCTGCTGCTTACCATTTGTCGCCGGTTGCCGGAGGCCATCGAGGAGGTGAAGAACGGTGGTTGGAC
CTCATGGAAACCCCTGTGGATGTGTGGCCACGGCCTTTCACAGAGCACCGTCGGCATCGTTGGCCTGGGGCGCATAGGCC
AGGCCATTGCTCGGCGTCTGAAACCATTCGGTGTCCGGAGATTTCTATACACAGGGCGCCAGCCCAGGTCTCAGGAAGCA
GCGGAATTCCAGGCAGAGTTTGTGTCCACCCCCGAGCTGGCCGCCGAGTCCGATTTCATCGTTGTGGCCTGCTCCTTAAC
ACCGGCGACCAGGGGGCTCTGCAACAAGGACTTCTTCCAGTGGATGAAGAAAACAGCTGTGTTTGTCAACATCAGCAGGG
GAGAAGTGGTAGACCAGGATGACCTGTACCAGGCCCTGGCCAGCGGTCAGATTGCAGCTGCTGGACTGGACGTGACGACC
CCAGAACCACTGCCTACCAACCACCCTCTCCTGACCCTGAAGAACTGTGTGATCTTGCCTCACATTGGCAGTGCCACCCA
CAGGACCCGAAACATCATGTCTGTCTTGGCAGCTGACAACCTGCTGGCTGGCCTGCGAGGGGAGCCGATGCCCAGTGAAC
TCAAGCTG

Alignment

ORF - retro_btau_636 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.99 %
• Parental protein coverage: 90.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QWDSDEPIPREDLEQRMAGAQGLLCLLSDRIDKKLLDAAGANLKVISTMSVGVDHLALDEIKKRGIRVGY
          QWDSDEPIPREDLEQRMAGAQGLLCLLSDRIDKKLLDAAGANLKVISTMSVGVDHLALDEIKKRGIRVGY
Retrocopy QWDSDEPIPREDLEQRMAGAQGLLCLLSDRIDKKLLDAAGANLKVISTMSVGVDHLALDEIKKRGIRVGY

Parental  TPGVLTDATAELAVSLLLTTCRRLPEAIEEVKNGGWTSWKPLWMCGHGLSQSTVGIVGLGRIGQAIARRL
          TPGVLTDATAELAVSLLLT.CRRLPEAIEEVKNGGWTSWKPLWMCGHGLSQSTVGIVGLGRIGQAIARRL
Retrocopy TPGVLTDATAELAVSLLLTICRRLPEAIEEVKNGGWTSWKPLWMCGHGLSQSTVGIVGLGRIGQAIARRL

Parental  KPFGVRRFLYTGRQPRPQEAAEFQAEFVSTPKLAAESDFIVVACSLTPATRGLCNKDFFQWMKKTAVFVN
          KPFGVRRFLYTGRQPR.QEAAEFQAEFVSTP.LAAESDFIVVACSLTPATRGLCNKDFFQWMKKTAVFVN
Retrocopy KPFGVRRFLYTGRQPRSQEAAEFQAEFVSTPELAAESDFIVVACSLTPATRGLCNKDFFQWMKKTAVFVN

Parental  ISRGEVVDQDDLYQALASGQIAAAGLDVTTPEPLPTNHPLLTLKNCVILPHIGSATHRTRNIMSVLAADN
          ISRGEVVDQDDLYQALASGQIAAAGLDVTTPEPLPTNHPLLTLKNCVILPHIGSATHRTRNIMSVLAADN
Retrocopy ISRGEVVDQDDLYQALASGQIAAAGLDVTTPEPLPTNHPLLTLKNCVILPHIGSATHRTRNIMSVLAADN

Parental  LLAGLRGEPMPSELKL
          LLAGLRGEPMPSELKL
Retrocopy LLAGLRGEPMPSELKL

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	1.37 RPM	20.40 RPM
ERP005899_muscle	0.53 RPM	13.67 RPM
SRP017611_brain	1.05 RPM	11.10 RPM
SRP017611_kidney	6.40 RPM	47.77 RPM
SRP017611_liver	3.85 RPM	61.99 RPM
SRP030211_testis	0.08 RPM	4.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_636 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_636 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_636 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019299	1 retrocopy	retro_btau_636 ,