RetrogeneDB ID: retro_btau_1646

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:32173941..32174783(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BT.58955
• Ensembl ID: ENSBTAG00000007817
• Aliases: None
• Description: lys-63-specific deubiquitinase BRCC36 [Source:RefSeq peptide;Acc:NP_001069258]

Sequence

>retro_btau_1646
ATACAAATAGTTCATCTGGAGTCCAGATGCTTTCCTACTATGTCTCAACCACACTCTGAACACAGAGAAAGAAGAGGTGA
TGGGGCTGTGCATAGAATTGAATGATGACTTAAGGAGTGACCCCAAGTTTACATATACTAGAACTGAAATCCACACAGTT
GCTGAAAAGTTTGACACTGTCAGAATTGTTCACATTCATTTTGTCATTGTCTTGCGGCGTTCTGATAAGAGGAAGAGTGG
AGTGGAAATTTCTCCAGAGCAGCTGTCTGTGGCTTTAACTGAGATAGAGAGGTTGGCTAAACTAACCGGTGGTACCCTGA
GAGTTGTGGGCTGGTATCATTCCCATCCCCATATAACGGTTAGGCCTTCCCATGTTGATGTTCACACACAAGCCATGTAA
CAGATTATGGAGCAAAGCTTTGTAGGGCTTGTATTTTTTTGTTTCCTCTAAGATAAAAATACAAAGATTGGACAGGTACT
CTATACTTGCTTTCAATCCATTAAGGCCCAAAAGAGCTCAGAGTATAAGAGAATTGAAATCCCAATTCATATTGTACCCC
CATCAAACCACTGGGAAAGTGTGCCTTGAGTCAGCAATTGAGTTGCCCAAGATCCTGTATCAAGAGGGGCAAGATGCACA
TAGGAGGATCCACAGCCTTCCACATCTGGATTCAGTAACCAAGATCCATAATGGCTCAGTGTTTACTAAGAATCTGTGTA
GGTCAGCAGTCAGCAGACCTCTACTACAGTGGTTGGAGGACAGACTGGAGAGAAACCAAAAGCATTTACAGGAGTTGCAA
CAAGAAAAGAAACAGTTTATGCAAGAACTTTCTTCTCTAGAA

Alignment

ORF - retro_btau_1646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 97.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VQAVHLES-DAFLVCLNHALSTEKEEVMGLCIGELNDDLRNDPKFTYTGTEMRTVAEKVDTVRIVHIHSV
          .Q.VHLES.DAFL.CLNH.L.TEKEEVMGLCI.ELNDDLR.DPKFTYT.TE..TVAEK.DTVRIVHIH.V
Retrocopy IQIVHLES>DAFLLCLNHTLNTEKEEVMGLCI-ELNDDLRSDPKFTYTRTEIHTVAEKFDTVRIVHIHFV

Parental  IILRRSDKRKDRVEISPEQLSAASTETHRLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQ
          I.LRRSDKRK..VEISPEQLS.A.TE..RLA.LTG...RVVGWYHSHPHITV.PSHVDV.TQAM.Q.M.Q
Retrocopy IVLRRSDKRKSGVEISPEQLSVALTEIERLAKLTGGTLRVVGWYHSHPHITVRPSHVDVHTQAM*QIMEQ

Parental  GFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSEYERIEIPIHIV-PHVTIGKVCLESAVELPKILCQ
          .FVGL.F.CF..DKNTK.G.VLYTCFQSI.AQKSSEY.RIEIPIHIV.PH.T.GKVCLESA.ELPKIL.Q
Retrocopy SFVGLVFFCFL*DKNTKIGQVLYTCFQSIKAQKSSEYKRIEIPIHIV>PHQTTGKVCLESAIELPKILYQ

Parental  EEQDAYRRIHSLTHLDSVTKIHNGSVFTKNLCSQMSAVSGPLLQWLEDRLEQNQQHVQELQQEKEELLQE
          E.QDA.RRIHSL.HLDSVTKIHNGSVFTKNLC...SAVS.PLLQWLEDRLE.NQ.H.QELQQEK....QE
Retrocopy EGQDAHRRIHSLPHLDSVTKIHNGSVFTKNLC--RSAVSRPLLQWLEDRLERNQKHLQELQQEKKQFMQE

Parental  LSSLE
          LSSLE
Retrocopy LSSLE

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	0.00 RPM	15.00 RPM
ERP005899_muscle	0.00 RPM	12.19 RPM
SRP017611_brain	0.00 RPM	11.15 RPM
SRP017611_kidney	0.00 RPM	14.28 RPM
SRP017611_liver	0.00 RPM	13.82 RPM
SRP030211_testis	0.02 RPM	1.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1646 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1646 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1646 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646 ,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,
Ictidomys tridecemlineatus	ENSSTOG00000019781	2 retrocopies	retro_itri_1271, retro_itri_806,