RetrogeneDB ID: retro_btau_526

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:47904562..47905533(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000020668
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM59
• Ensembl ID: ENSBTAG00000009526
• Aliases: None
• Description: transmembrane protein 59 precursor [Source:RefSeq peptide;Acc:NP_001030248]

Sequence

>retro_btau_526
ATGGCGCTGCCGAAGGGGAGCCTATGGCTCAGGGCCCAACTGGGGATCCCGCCGCTACTGCTGCTGGCCATGGCCCTGGC
CGGAGGCTCGGAAACCGCTTCGGCTGAAGCATTTGACTCGGTGTTGGGTGATACGGGGTCTTGTCACCGGGCCTGTCAGT
TGATGTATCCCTTGCACACCTACCCCAAGGAAGAGGAGTTGTATGCATGTCAGAGAGGTTGCAGGCTGTTTTCAATTTGT
CAGTTTGTGATGATGGAATTGATTTAAATCGGACCAAATTGGAATGTGAATCTGCATGTACAGAAGCATATTCCCAATCT
GATGAGCAATATGCTTGCCATCTTGGTTGCCAGAATCAGCTGCCATACACAGAATTGAGACAAGAACAACTCATGTCCCT
GATGCCAAAAATGCATCTACTCTTCCCTCTAACTCTGGTAAGATCATTCTGGAGTGATATGGTGGACTCTGCACAGAGCT
TCATAACCTCTTCGTGGACTTTTTATCTTCAAGCTGATGATGGAAAAATAGTTATATTCCAGTCTAAGCCAGAAATCCAG
TATGCACCACAGTTGGAGCAGGAGCCTACAAAATTGAAAGACTCATCACTAAGCAAAATGTCCTCAGATCTGCAAATGAG
AAGTTCACAAGCACATAGAAACTATCTTGAAGATGGAGAAAGTGACGGCTTTTTAAGATGCCTGGCTCTTAACTCTGGGT
GGATTTTAACCGTGACTCTTGTCCTCTCTGTGATGGTGTTGCTCTGGATTTGCTGTGCAACTGTTGCTACAGCTGTGCAG
CAGTATGTTCCCTCTGAGAAGCTGAGTATCTATGGTGACTTGGAATTTATGAATGAACAAAAGCTAAACAGATATCCAGC
TTCTTCTCTTGTGGTTGTTAGATCTAAAGCTGAAGATCATGAAGAAGCAGGGCCTCTACCTGCAAAAGTGAATCTTGCTC
ATTCAGAAATC

Alignment

ORF - retro_btau_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVPKGSLWLRAQLGIPPLLLLAMALAGGSGTASAEAFDSVLGDTASCHRACQLTYPLHTYPKEEELYAC
          MA.PKGSLWLRAQLGIPPLLLLAMALAGGS.TASAEAFDSVLGDT.SCHRACQL.YPLHTYPKEEELYAC
Retrocopy MALPKGSLWLRAQLGIPPLLLLAMALAGGSETASAEAFDSVLGDTGSCHRACQLMYPLHTYPKEEELYAC

Parental  QRGCRLFSICQFV-DDGIDLNRTKLECESACTEAYSQSDEQYACHLGCQNQLPYAELRQEQLMSLMPKMH
          QRGCRLFSICQFV.DDGIDLNRTKLECESACTEAYSQSDEQYACHLGCQNQLPY.ELRQEQLMSLMPKMH
Retrocopy QRGCRLFSICQFV<DDGIDLNRTKLECESACTEAYSQSDEQYACHLGCQNQLPYTELRQEQLMSLMPKMH

Parental  LLFPLTLVRSFWSDMVDSAQSFITSSWTFYLQADDGKIVIFQSKPEIQYAPQLEQEPTNLKDSSLSKMSY
          LLFPLTLVRSFWSDMVDSAQSFITSSWTFYLQADDGKIVIFQSKPEIQYAPQLEQEPT.LKDSSLSKMS.
Retrocopy LLFPLTLVRSFWSDMVDSAQSFITSSWTFYLQADDGKIVIFQSKPEIQYAPQLEQEPTKLKDSSLSKMSS

Parental  -LQMRSSQAHRNYLEDGESDGFLRCLSLNSGWILTVTLVLSVMVLLWICCATVATAVEQYVPSEKLSIYG
          .LQMRSSQAHRNYLEDGESDGFLRCL.LNSGWILTVTLVLSVMVLLWICCATVATAV.QYVPSEKLSIYG
Retrocopy DLQMRSSQAHRNYLEDGESDGFLRCLALNSGWILTVTLVLSVMVLLWICCATVATAVQQYVPSEKLSIYG

Parental  DLEFMNEQKLNRYPASSLVVVRSKAEDHEEAGPLPAKVNLAHSEI
          DLEFMNEQKLNRYPASSLVVVRSKAEDHEEAGPLPAKVNLAHSEI
Retrocopy DLEFMNEQKLNRYPASSLVVVRSKAEDHEEAGPLPAKVNLAHSEI

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	4.40 RPM	172.53 RPM
ERP005899_muscle	1.00 RPM	170.35 RPM
SRP017611_brain	2.70 RPM	70.07 RPM
SRP017611_kidney	3.38 RPM	148.77 RPM
SRP017611_liver	5.13 RPM	109.79 RPM
SRP030211_testis	0.51 RPM	110.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_526 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_526 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009526	1 retrocopy	retro_btau_526 ,
Felis catus	ENSFCAG00000007737	1 retrocopy	retro_fcat_433,
Tursiops truncatus	ENSTTRG00000003198	3 retrocopies	retro_ttru_1079, retro_ttru_1723, retro_ttru_332,