RetrogeneDB ID: retro_btau_513

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:43280031..43281469(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000035572
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.61946
• Ensembl ID: ENSBTAG00000003450
• Aliases: ATP6V1H, SFD
• Description: V-type proton ATPase subunit H [Source:RefSeq peptide;Acc:NP_777129]

Sequence

>retro_btau_513
ATGACCAAGATGGATATTCGGGGCGCTGTGGATGCTGCTGTTCCCAACAACATCATTGCCGCCAAGGCTGCGGAAGTCCG
TGCGAACAAAGTGAACTGGCAGTCCTACCTGCAGGGGCAGATGATTTCTTCTGAAGACTGCGAGTTCATTCAAAGATTTG
AGATGAAAAGAAGTCCTGAGGAGAAGCAGGAGATGCTTCAGACTGAAGGCAGTCAGTGTGCTAAGACATTTATAAATCGG
ATGACTCCTATTTCCAAAGAGCAGACCAGTTCAGTACATACTCACCCTGGTGGATGATACACTGCAGGAAAATCACCAGC
GTGTTAGCATTTTCTTTGACTATGCTAAACGTAGCAAGAACACTGCCTGGTCCTACTTCCTGCCGATGCTGAATCGCCAG
GATCTCTTTACTGTTCGTATGGCAGCAAGAATTATTGCCAAGTTACCAGCTTGGGGAAAAGAACTGATGAAAGGCAGCGA
CTTGAATTACTATTTCAATTGGATAAAGACTCAACTAAGTTCACAGAAACTGTGTGGTAGCGGTATCGCTGCTGAAACAG
AAACAGTCTCTTCAAGCGATAGTTCCCAGTATGTGCAGTGCGTGGCCGGGTGTCTGCAGCTGATGCTCCGAGTCAATGAG
TACCGCTTCGCCTGGGTGGAGGCAGACGGGGTGAACTGCATCATGGGCGTTCTGAGTAACAAGTGTGGCTTTCAGCTCCA
GTATCAGATGATCTTTTCCGTGTGGCTCCTGGCTTTCAGCCCACAGATGTGTGAACACCTGAGGCGCTACAACATCATCC
CTGTCCTGTCCGACATCCTGCAGGAGTCGGTCAAAGAGAAGGTGACGAGGATCATCCTCGCAGCATTCCGTAACTTCTTA
GAAAAGTCAGTTGAACGAGAAACTCGCCAAGAGTATGCCCTGGCGATGATTCAGTGCAAAGTCCTGAAACAGCTGGAGAA
CTTGGAGCAGCAGAAGTACGACGAAGACATCAGTGAGGATATAAAGTTCCTCTTGGAGAAACTCGGTGAAAGTGTCCAGG
ATCTCAGCTCATTTGATGAATACAGTTCAGAACTAAAGTCTGGGAGGTTGGAGTGTAGTCCTGTGCACAAATCTGAGAAA
TTTTGGAGAGAGAATGCTGCGAGGTTAAATGAAAAGAATGATGAGCTCTTGAAAATTTTGACCGAACTTCTGGAGGTGTC
TGACGATCCCCAAGTCTTAGCTGTTGCCGCCCATGACGCTGGGGTGTATGTGCGCCATTACCCACGAGGCAAGCGGGTCA
TGGAACAGCTGGGTGGGAAGCAGCGGGTGATGAACCACGAGGACCAGCAGGTGCGCTACAACGCCCTCCTGGCTGTACAG
AAGCTCATGGTGCACAACTGGGAATATCTTGGTAAACAACTCCAGTCTGAACAGCCGCAGACTGCAGCTGCCCGGAGC

Alignment

ORF - retro_btau_513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTKMDIRGAVDAAVPTNIIAAKAAEVRANKVNWQSYLQGQMISSEDCEFIQRFEMKRSPEEKQEMLQTEG
          MTKMDIRGAVDAAVP.NIIAAKAAEVRANKVNWQSYLQGQMISSEDCEFIQRFEMKRSPEEKQEMLQTEG
Retrocopy MTKMDIRGAVDAAVPNNIIAAKAAEVRANKVNWQSYLQGQMISSEDCEFIQRFEMKRSPEEKQEMLQTEG

Parental  SQCAKTFINLMTHISKEQT-VQYILTLVDDTLQENHQRVSIFFDYAKRSKNTAWSYFLPMLNRQDLFTVH
          SQCAKTFIN.MT.ISKEQT.VQYILTLVDDTLQENHQRVSIFFDYAKRSKNTAWSYFLPMLNRQDLFTV.
Retrocopy SQCAKTFINRMTPISKEQT>VQYILTLVDDTLQENHQRVSIFFDYAKRSKNTAWSYFLPMLNRQDLFTVR

Parental  MAARIIAKLAAWGKELMEGSDLNYYFNWIKTQLSSQKLRGSGVTAETGTVSSSDSSQYVQCVAGCLQLML
          MAARIIAKL.AWGKELM.GSDLNYYFNWIKTQLSSQKL.GSG..AET.TVSSSDSSQYVQCVAGCLQLML
Retrocopy MAARIIAKLPAWGKELMKGSDLNYYFNWIKTQLSSQKLCGSGIAAETETVSSSDSSQYVQCVAGCLQLML

Parental  RVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSVWLLAFSPQMCEHLRRYNIIPVLSDILQESVKE
          RVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSVWLLAFSPQMCEHLRRYNIIPVLSDILQESVKE
Retrocopy RVNEYRFAWVEADGVNCIMGVLSNKCGFQLQYQMIFSVWLLAFSPQMCEHLRRYNIIPVLSDILQESVKE

Parental  KVTRIILAAFRNFLEKSVERETRQEYALAMIQCKVLKQLENLEQQKYDDEDISEDIKFLLEKLGESVQDL
          KVTRIILAAFRNFLEKSVERETRQEYALAMIQCKVLKQLENLEQQKYD.EDISEDIKFLLEKLGESVQDL
Retrocopy KVTRIILAAFRNFLEKSVERETRQEYALAMIQCKVLKQLENLEQQKYD-EDISEDIKFLLEKLGESVQDL

Parental  SSFDEYSSELKSGRLEWSPVHKSEKFWRENAARLNEKNYELLKILTKLLEVSDDPQVLAVAAHDVGEYVR
          SSFDEYSSELKSGRLE.SPVHKSEKFWRENAARLNEKN.ELLKILT.LLEVSDDPQVLAVAAHD.G.YVR
Retrocopy SSFDEYSSELKSGRLECSPVHKSEKFWRENAARLNEKNDELLKILTELLEVSDDPQVLAVAAHDAGVYVR

Parental  HYPRGKRVIEQLGGKQLVMNHMHHEDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS
          HYPRGKRV.EQLGGKQ.VMNH...EDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS
Retrocopy HYPRGKRVMEQLGGKQRVMNH---EDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAAARS

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	0.14 RPM	11.54 RPM
ERP005899_muscle	0.37 RPM	23.07 RPM
SRP017611_brain	0.82 RPM	108.90 RPM
SRP017611_kidney	0.89 RPM	73.62 RPM
SRP017611_liver	0.08 RPM	10.42 RPM
SRP030211_testis	2.21 RPM	59.63 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_513 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_513 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	ENSBTAG00000003450	1 retrocopy	retro_btau_513 ,