RetrogeneDB ID: retro_btau_82

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:92648161..92649478(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000039391
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: USP22
• Ensembl ID: ENSBTAG00000008978
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase 22 [Source:UniProtKB/Swiss-Prot;Acc:P0C8Z3]

Sequence

>retro_btau_82
ATGTGTAAGGACTATGTATATGACAGAGACATTGAGCAAATTGCCAAAGAAGAGCAAGGGGAAGCTTTGAAATTACAAGC
CTCCACCTCGACCGAGGTTTCTCACCAGCAGTATTCAGTGCCAGGCCTCGGTGAGAAGTATCCAACCTGGGAGACAACCA
AACCTGAGTTAGAACTGCTGGGCCATAACCCAAGGAGAAGAAGAATCGCCTCCAGCTTTACCATCGGTTTAAGAGGACTG
ATCAATCTTGGCAACACGTGCTTTATGAACTGCATCGTCCAGGCCCTTACCCACACTCCGATCCTGAGAGATTTCTTCCT
CTCTGACAGGCACAGATGTGAAATGCCGAGTCCGGAGTTGTGTCTGGTCTGTGAGATGTCTTCGCTTTTTCGAGAGTTGT
ATTCTGGAAACCCATCTCCTCATGTTCCCTATAAGTTACTGCACCTGGTATGGATACACGCACGGCATTTAGCAGGGTAC
AGGCAACAGGATGCACATGAGTTTCTCATTGCAGCGTTAGATGTCCTGCACAGGCACTGCAAAGGTGATGATGCTGGGAA
GGCGGCCAGCAATCCCAACCACTGTAACTGCATCATTGACCAAATTTTCACAGGTGGCCTGCAATCTGATGTCACCTGTC
AAGCCTGTCATGGTGTCTCCACCACAATAGACCCATGCTGGGACATCAGTTTGGACTTGCCTGGCTCTTGTACCTCCTTC
TGGCCGATGAGCCCAGGGAGGGAGAGCAGTGTTAACGGGGAAAGCCACATACCAGGAATCACTACCCTCACGGACTGTCT
GCGAAGGTTTACGAGGCCAGAGCACTTAGGAAGCAGTGCCAAAATCAAGTGTGGTAGTTGCCAAAGCTACCAGGAATCTA
CCAAACAGCTCACAATGAATAAATTACCTGTCGTTGCCTGTTTTCATTTCAAACGGTTTGAACACTCAGCCAAACAGAGG
CGCAAGATCACTACATACATATCCTTTCCTCTGGAGCTGGATATGACACCTTTCATGGCCTCGAGTAAAGAGAGCAGGAT
GAATGGACAGTTGCAGCTGCCAACCAATAGTGGAAACGATGAGAATAAGTATTCCTTGTTTGCTGTGGTTAATCACCAAG
GAACCTTGGAGAGTGGCCACTACACCAGCTTCATCCGGCACCACAAGGACCAGTGGTTCAAGTGTGATGATGCCGTCATC
ACCAAGGCCAGTATTAAGGACGTGCTGGACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGTCCTGGAACACGAATC
AGAAAAAGTGAAAGAAGTGAATACACAAGCCTACTGA

Alignment

ORF - retro_btau_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.09 %
• Parental protein coverage: 77.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEQRKAWKMQGVGEKFSTWEPTKRELELLKHNPKRRKITSNCTIGLRGLINLGNTCFMNCIVQALTHTPL
          E.........G.GEK..TWE.TK.ELELL.HNP.RR.I.S..TIGLRGLINLGNTCFMNCIVQALTHTP.
Retrocopy EVSHQQYSVPGLGEKYPTWETTKPELELLGHNPRRRRIASSFTIGLRGLINLGNTCFMNCIVQALTHTPI

Parental  LRDFFLSDRHRCEMQSPSSCLVCEMSSLFQEFYSGHRSPHIPYKLLHLVWTHARHLAGYEQQDAHEFLIA
          LRDFFLSDRHRCEM.SP..CLVCEMSSLF.E.YSG..SPH.PYKLLHLVW.HARHLAGY.QQDAHEFLIA
Retrocopy LRDFFLSDRHRCEMPSPELCLVCEMSSLFRELYSGNPSPHVPYKLLHLVWIHARHLAGYRQQDAHEFLIA

Parental  ALDVLHRHCKGDDNGKKANNPNHCNCIIDQIFTGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFW
          ALDVLHRHCKGDD.GK.A.NPNHCNCIIDQIFTGGLQSDVTCQ.CHGVSTTIDP.WDISLDLPGS.T.FW
Retrocopy ALDVLHRHCKGDDAGKAASNPNHCNCIIDQIFTGGLQSDVTCQACHGVSTTIDPCWDISLDLPGSCTSFW

Parental  PLSPGSESSVVNGESHVSGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHL
          P.SPG.ESS.VNGESH..G.TTLTDCLRRFTRPEHLGSSAKIKC..C.SYQESTKQLTM.KLP.VACFH.
Retrocopy PMSPGRESS-VNGESHIPGITTLTDCLRRFTRPEHLGSSAKIKCGSCQSYQESTKQLTMNKLPVVACFHF

Parental  KRFEHSAKLRRKITTYVSFPLELDMTPFMASSKESRMNGQYQQPTDSLNNDNKYSLFAVVNHQGTLESGH
          KRFEHSAK.RRKITTY.SFPLELDMTPFMASSKESRMNGQ.Q.PT.S.N..NKYSLFAVVNHQGTLESGH
Retrocopy KRFEHSAKQRRKITTYISFPLELDMTPFMASSKESRMNGQLQLPTNSGNDENKYSLFAVVNHQGTLESGH

Parental  YTSFIRQHKDQWFKCDDAIITKASIADVLDSEGYLLFYHKQFLEYE
          YTSFIR.HKDQWFKCDDA.ITKASI.DVLDSEGYLLFYHKQ.LE.E
Retrocopy YTSFIRHHKDQWFKCDDAVITKASIKDVLDSEGYLLFYHKQVLEHE

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	1.01 RPM	43.11 RPM
ERP005899_muscle	0.53 RPM	208.62 RPM
SRP017611_brain	6.21 RPM	287.92 RPM
SRP017611_kidney	23.18 RPM	361.08 RPM
SRP017611_liver	0.76 RPM	98.84 RPM
SRP030211_testis	8.11 RPM	66.06 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_82 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_82 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_82 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008978	1 retrocopy	retro_btau_82 ,
Canis familiaris	ENSCAFG00000018523	1 retrocopy	retro_cfam_125,
Homo sapiens	ENSG00000124422	1 retrocopy	retro_hsap_26,
Microcebus murinus	ENSMICG00000009998	1 retrocopy	retro_mmur_1,
Mus musculus	ENSMUSG00000042506	1 retrocopy	retro_mmus_239,
Otolemur garnettii	ENSOGAG00000015801	1 retrocopy	retro_ogar_274,
Pan troglodytes	ENSPTRG00000008891	1 retrocopy	retro_ptro_44,
Pteropus vampyrus	ENSPVAG00000001934	1 retrocopy	retro_pvam_905,
Ictidomys tridecemlineatus	ENSSTOG00000023814	1 retrocopy	retro_itri_163,