RetrogeneDB ID: retro_mmus_239

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:7373544..7374861(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000046269
• Aliases: Usp27x, Sfc11, Usp27
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Usp22
• Ensembl ID: ENSMUSG00000042506
• Aliases: Usp22, AI427806
• Description: ubiquitin specific peptidase 22 [Source:MGI Symbol;Acc:MGI:2144157]

Sequence

>retro_mmus_239
ATGTGTAAAGACTATGTGTATGACATAGACATTGAGCAAATTGCCAAAGAAGAGCAAGGAGAAGCCTTGAAATTACAAGC
GTCCACCTCGACAGAGGTTTCTCAGCAACAGTGTTCAGTGCCGGGACTTGGGGAGAAATATCCCACCTGGGAAACGACCA
AACCTGAACTAGAACTTCTGGGGCACAACCCACGGAGAAGAAGGATCGCCTCCAGCTTTACCATCGGCTTACGAGGACTA
ATTAATCTTGGCAACACGTGTTTTATGAACTGCATTGTCCAGGCCTTGACCCACACTCCAATACTGAGAGATTTCTTTCT
CTCTGACAGGCACCGGTGTGAAATGCCCAGCCCTGAGTTGTGTCTGGTCTGTGAGATGTCGTCGCTCTTTCGGGAGCTGT
ATTCTGGAAACCCATCTCCTCATGTGCCCTATAAGTTACTGCACCTGGTGTGGATACACGCTCGTCATCTAGCAGGGTAC
AGGCAGCAGGATGCCCACGAGTTCCTCATCGCTGCGCTAGATGTCCTGCATAGGCACTGCAAAGGTGACGATGTTGGCAA
GGTGGCCAGCAACCCCAACCACTGTAACTGCATCATAGACCAAATCTTCACAGGTGGCCTGCAGTCCGATGTCACCTGTC
AAGCCTGCCATGGTGTCTCCACCACTATAGACCCATGCTGGGACATTAGTCTGGACTTGCCTGGCTCTTGCACATCCTTC
TGGCCCATGAGCCCTGGGAGGGAGAGCAGTTTGAATGGCGAAAGCCACATCCCAGGCATCACCACTCTCACGGACTGCTT
GCGAAGGTTTACAAGGCCAGAGCACTTAGGAAGTAGTGCCAAAATCAAGTGTGGTAGTTGCCAAAGCTACCAAGAATCTA
CCAAACAGCTCACTATGAAGAAGTTACCAGTAGTTGCCTGCTTTCATTTCAAACGGTTTGAACACTCAGCGAAACAGAGG
CGCAAGATCACTACGTACATTTCCTTTCCTCTGGAGCTGGATATGACACCATTTATGGCGTCAAGTAAAGAGACCCGGGT
GAATGGACAGTTGCAGCTCCCAACCAATAGTGCGAACAACGAGAATAAGTATTCCTTGTTTGCTGTGGTTAATCACCAAG
GAACCTTGGAGAGTGGCCACTACACCAGCTTCATTCGGCACCACAGGGACCAGTGGTTCAAGTGTGATGATGCCGTAATC
ACCAAGGCCAGTATTAAGGATGTGCTGGACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGTCCTGGAACCTGAGCC
AGAAAAGGTGAAAGAAATGACTCCACAAGCCTACTGA

Alignment

ORF - retro_mmus_239 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 75.43 %
• 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 EVSQQQCSVPGLGEKYPTWETTKPELELLGHNPRRRRIASSFTIGLRGLINLGNTCFMNCIVQALTHTPI

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

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

Parental  PLSPGSEGSVVNGESHASGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHL
          P.SPG.E.S..NGESH..G.TTLTDCLRRFTRPEHLGSSAKIKC..C.SYQESTKQLTMKKLP.VACFH.
Retrocopy PMSPGRESS-LNGESHIPGITTLTDCLRRFTRPEHLGSSAKIKCGSCQSYQESTKQLTMKKLPVVACFHF

Parental  KRFEHSAKLRRKITTYVSFPLELDMTPFMASSKESRMNGQYQQPLDSLNNDNKYSLFAVVNHQGTLESGH
          KRFEHSAK.RRKITTY.SFPLELDMTPFMASSKE.R.NGQ.Q.P..S.NN.NKYSLFAVVNHQGTLESGH
Retrocopy KRFEHSAKQRRKITTYISFPLELDMTPFMASSKETRVNGQLQLPTNSANNENKYSLFAVVNHQGTLESGH

Parental  YTSFIRQHKDQWFKCDDAIITKASIKDVLDSEGYLLFYHKQFLEYE
          YTSFIR.H.DQWFKCDDA.ITKASIKDVLDSEGYLLFYHKQ.LE.E
Retrocopy YTSFIRHHRDQWFKCDDAVITKASIKDVLDSEGYLLFYHKQVLEPE

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
SRP007412_brain	9.93 RPM	271.92 RPM
SRP007412_cerebellum	4.69 RPM	202.78 RPM
SRP007412_heart	0.62 RPM	39.78 RPM
SRP007412_kidney	1.42 RPM	48.97 RPM
SRP007412_liver	0.44 RPM	36.27 RPM
SRP007412_testis	2.47 RPM	23.92 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_239 in 4 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	X:7375675..7376095
ENCFF001YIJ	POLR2A	X:7375592..7376611
ENCFF001YJZ	POLR2A	X:7375562..7376981
ENCFF001YKA	POLR2A	X:7375585..7377066

EST

No EST(s) were mapped for retro_mmus_239 retrocopy.

TSS

No TSS is located nearby retro_mmus_239 retrocopy 5' end.

Lab

retro_mmus_239 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_239 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_26

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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,