RetrogeneDB ID: retro_btau_637

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:9512155..9514159(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000020953
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.61431
• Ensembl ID: ENSBTAG00000018361
• Aliases: None
• Description: R3H domain-containing protein 2 [Source:RefSeq peptide;Acc:NP_001071502]

Sequence

>retro_btau_637
AACCGTGAGGGGCTGAGCCGCACCTCAAGCAGCTGCCAGAGCAGCACAGACAGCGAACTCAAATCCCTGGAGCAGCACGG
ACTCCGATGGCTCTCTCCGGAGCATGCGGCCCCCTGTCACCAAAGCCAGCAGCTTCAGTGGAATCTCCATCCTCACCCGG
GGTGACAGCATTGGGAGCAGCAAAGGTGGCAGTGCAGGAAGGATTTCCAGGCCAGGTATGGCACTAGGTGCCCCAGAAGT
GTGCAACCAGGTCACCTCATCCCAGTCTGTCTGGGCCTTCTCCCTTGTACTGCCCAACAACAGCAGCAGCAGCAACTTCC
TGCTCTCCCACCCATGCCTCAACAACAGCCACCCTTGAATAATCACATGATTTCACAGGCAGATGATCTCAGCAACCCCT
TTGGACAAATGAGCCTTAGTCGCCAAGGTTCTACTGAAGCAGCTGACCCATCCTCAGCTCTGTTCCAGTCCCCACTTATC
TCCCAGCACCCTCAGCAGACTAGCTTCATCATGGCTTCTACAGGGCAGCCCCTCCCTACTTCCAACTATTCCACCTTTAG
CCATGCACCACCTACTCAGCAAGTCCTGCCACCCCAGGGCTACATGCAGCCCCCTCAACAGACCCAGGTGTCTTACTGTT
CCCCTGGACAGTACCCCAACTCCAACCAGCAATACCGACCTCTGTCTCACCCGGTGGCATACAGCCCCCAGCGTGGTCAG
CAGCTGCCTCAGCCATCCCAGAAGCCTGGTTTACAGCCCATGATGCCTAACCAGCAGCAAGCGGCTTACCAAGGCATGAT
TGGGGTCCAGCAGCCACAGAACCAGGGCCTGCTCAGCAACCAGAGGAGCGGCATTGGGGGCCAGATGCAAGGCCTGGTGG
TTCAGTACACTCCACTGCCTTCTTACCAAGTCCCAGTGGGTAATGACTCACAAAATATGGTCCAGCCACCTTTCCAGCAA
CCCATGCTGGTCCCTGCAAGCCAATCTGTGCAGGGGGCCCTCCCAGCAGGGGGTGTTCCAGTGTATTACAGCATGATCCC
GCCAGCTCAGCAGAATGGTACAAGCCCTTCTGTGGGGTTTCTGCAGCCTCCTGGCTCTGAGCAGTACCAGATGCCTCAGT
CTCCCTCCCCCTGCAGTCCACCACAGATGCCACAGCAGTACTCAGGAGTGTCACCTTCTGGACCAGGTGTGGTGGTCATG
CAGCTGAATGTCCCTAATGGACCCCAGCCTCCCCAGAACCCATCCATGGTCCAGTGGAGTCACTGTAAATATTACAGCAT
GGACCAGCGGGGTCAGAAACCTGGAGACCTGTACAGTCCTGAGAGCAGCCCCCAGGCCAACACACAGATGAGCAGCAGCC
CTGTCACATCTCCTACTCAGTCTCCAGCACCCTCTCCTGTCACCAGCCTCAGCAACGTCTGCACAGGACTTAGTCCCCTT
CCTGTCCTCACACAGTTCCCCCGGCCTGGAGGTCCCGCACAGGGTGATGGTCGCTATTCCCTCTTGGGCCAGCCGTTACA
GTACAATCTGTCCATCTGCCCTCCCCTGCTCCATGGCCAGTCAGCTTACTCGGTGCACCAGGGACAGAGCGGATTGAAGC
ATGGAAATCGGAGCAAGAGACAAGCACTCAAATCTGCCTCCACTGACTTGGGGACAACAGACGTTGTTCTGGGACGGATA
CTGGAGGTGACAGATCTCCCGGAGGGCATCACCCGTACCGAGGCAGACAAACACTTCACTCAGCTTGCCATGTCCGGTGC
CAAGATCCAGTGGCTCAAGGATGCTCAGGGGCTGCCCGGTGGGGGTGGGGGGGACAACGGTGGGACTGCTGAGAATGGCC
GCCACTCGGACCTCGCTGCCTTGTACACCATTGTGGCTGTGTTCCCCAGCCCCCTGGCTGCTCAGAATGCCTCCCTTCGC
CTCAACAACTCTGTGAGTCGCTTCAAACTTCGAGTGGCCAAAAAGAACTATGACCTGAGGATCCTGGAGGGAGCCAGCTC
CCAA

Alignment

ORF - retro_btau_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 67.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRTSSSRQSSTDSELKSLEPR-PWSSTDSDGSVRSMRPPVTKASSFSGISILTRGDSIGSSKGGSAGRIS
          .R...SR.SS........E...PWSSTDSDGS.RSMRPPVTKASSFSGISILTRGDSIGSSKGGSAGRIS
Retrocopy NREGLSRTSSSCQSSTDSELK>PWSSTDSDGSLRSMRPPVTKASSFSGISILTRGDSIGSSKGGSAGRIS

Parental  RPGMALGAPEVAT-MSSSQSV-RGLLPCTAQQQQQQPQPVPALQPSPQLSPPQQYNMISQADDLSNPFGQ
          RPGMALGAPEV.....SSQSV..GLLPCTAQQQQQQ....PAL.P.PQ..PP....MISQADDLSNPFGQ
Retrocopy RPGMALGAPEVCNQVTSSQSV<LGLLPCTAQQQQQQQ--LPALPPMPQQQPPLNNHMISQADDLSNPFGQ

Parental  MSLSRQGSTEAADPSSALFQPPLISQHPQQTSFIMASTGQPLPTSNYSTSSHAPPTQQVLPPQGYMQPPQ
          MSLSRQGSTEAADPSSALFQ.PLISQHPQQTSFIMASTGQPLPTSNYST.SHAPPTQQVLPPQGYMQPPQ
Retrocopy MSLSRQGSTEAADPSSALFQSPLISQHPQQTSFIMASTGQPLPTSNYSTFSHAPPTQQVLPPQGYMQPPQ

Parental  QIQVSYYSPGQYPNSNQQYRPLSHPVAYSPQRGQQLPQPSQQPGLQPMMPNQQQAAYQGMIGVQQPQNQG
          Q.QVSY.SPGQYPNSNQQYRPLSHPVAYSPQRGQQLPQPSQ.PGLQPMMPNQQQAAYQGMIGVQQPQNQG
Retrocopy QTQVSYCSPGQYPNSNQQYRPLSHPVAYSPQRGQQLPQPSQKPGLQPMMPNQQQAAYQGMIGVQQPQNQG

Parental  LLSNQRSGMGGQMQGLVVQYTPLPSYQVPVGNDSQNVVQPPFQQPMLVPASQSVQGALPAGGVPVYYSMI
          LLSNQRSG.GGQMQGLVVQYTPLPSYQVPVGNDSQN.VQPPFQQPMLVPASQSVQGALPAGGVPVYYSMI
Retrocopy LLSNQRSGIGGQMQGLVVQYTPLPSYQVPVGNDSQNMVQPPFQQPMLVPASQSVQGALPAGGVPVYYSMI

Parental  PPAQQNGTSPSVGFLQPPGSEQYQMPQSPSPCSPPQMPQQYSGVSPSGPGVVVMQLNVPNGPQPPQNPSM
          PPAQQNGTSPSVGFLQPPGSEQYQMPQSPSPCSPPQMPQQYSGVSPSGPGVVVMQLNVPNGPQPPQNPSM
Retrocopy PPAQQNGTSPSVGFLQPPGSEQYQMPQSPSPCSPPQMPQQYSGVSPSGPGVVVMQLNVPNGPQPPQNPSM

Parental  VQWSHCKYYSMDQRGQKPGDLYSPESSPQANTQMSSSPVTSPTQSPAPSPVTSLSNVCTGLSPLPVLTQF
          VQWSHCKYYSMDQRGQKPGDLYSPESSPQANTQMSSSPVTSPTQSPAPSPVTSLSNVCTGLSPLPVLTQF
Retrocopy VQWSHCKYYSMDQRGQKPGDLYSPESSPQANTQMSSSPVTSPTQSPAPSPVTSLSNVCTGLSPLPVLTQF

Parental  PRPGGPAQGDGRYSLLGQPLQYNLSICPPLLHGQSAYSVHQGQSGLKHGNRSKRQALKSASTDLGTTDVV
          PRPGGPAQGDGRYSLLGQPLQYNLSICPPLLHGQSAYSVHQGQSGLKHGNRSKRQALKSASTDLGTTDVV
Retrocopy PRPGGPAQGDGRYSLLGQPLQYNLSICPPLLHGQSAYSVHQGQSGLKHGNRSKRQALKSASTDLGTTDVV

Parental  LGRVLEVTDLPEGITRTEADKLFTQLAMSGAKIQWLKDAQGLPGGGGGDNGGTAENGRHSDLAALYTIVA
          LGR.LEVTDLPEGITRTEADK.FTQLAMSGAKIQWLKDAQGLPG.....NGGTAENGRHSDLAALYTIVA
Retrocopy LGRILEVTDLPEGITRTEADKHFTQLAMSGAKIQWLKDAQGLPGXXXXXNGGTAENGRHSDLAALYTIVA

Parental  VFPSPLAAQNASLRLNNSVSRFKLRVAKKNYDLRILERASSQ
          VFPSPLAAQNASLRLNNSVSRFKLRVAKKNYDLRILE.ASSQ
Retrocopy VFPSPLAAQNASLRLNNSVSRFKLRVAKKNYDLRILEGASSQ

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	0.50 RPM	21.99 RPM
ERP005899_muscle	2.75 RPM	35.32 RPM
SRP017611_brain	5.34 RPM	115.11 RPM
SRP017611_kidney	6.58 RPM	71.60 RPM
SRP017611_liver	2.42 RPM	24.92 RPM
SRP030211_testis	3.53 RPM	57.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_637 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_637 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018361	1 retrocopy	retro_btau_637 ,
Macaca mulatta	ENSMMUG00000021789	1 retrocopy	retro_mmul_1848,
Ictidomys tridecemlineatus	ENSSTOG00000020756	1 retrocopy	retro_itri_1550,