RetrogeneDB ID: retro_hsap_26

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:49644910..49646227(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000242013
• Aliases: USP27X, USP22L, USP27
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: USP22
• Ensembl ID: ENSG00000124422
• Aliases: USP22, USP3L
• Description: ubiquitin specific peptidase 22 [Source:HGNC Symbol;Acc:12621]

Sequence

>retro_hsap_26
ATGTGTAAGGACTATGTATATGACAAAGACATTGAGCAAATTGCCAAAGAAGAGCAAGGAGAAGCTTTGAAATTACAAGC
CTCCACCTCAACAGAGGTTTCTCACCAGCAGTGTTCAGTGCCAGGCCTTGGTGAGAAATTCCCAACCTGGGAAACAACCA
AACCAGAATTAGAACTGCTGGGGCACAACCCGAGGAGAAGAAGAATCACCTCCAGCTTTACGATCGGTTTAAGAGGACTC
ATCAATCTTGGCAACACGTGCTTTATGAACTGCATTGTCCAGGCCCTCACCCACACGCCGATACTGAGAGATTTCTTTCT
CTCTGACAGGCACCGATGTGAGATGCCGAGTCCCGAGTTGTGTCTGGTCTGTGAGATGTCGTCGCTGTTTCGGGAGTTGT
ATTCTGGAAACCCGTCTCCTCATGTGCCCTATAAGTTACTGCACCTGGTGTGGATACATGCCCGCCATTTAGCAGGGTAC
AGGCAACAGGATGCCCACGAGTTCCTCATTGCAGCGTTAGATGTCCTGCACAGGCACTGCAAAGGTGATGATGTCGGGAA
GGCGGCCAACAATCCCAACCACTGTAACTGCATCATAGACCAAATCTTCACAGGTGGCCTGCAGTCTGATGTCACCTGTC
AAGCCTGCCATGGCGTCTCCACCACGATAGACCCATGCTGGGACATTAGTTTGGACTTGCCTGGCTCTTGCACCTCCTTC
TGGCCCATGAGCCCAGGGAGGGAGAGCAGTGTGAACGGGGAAAGCCACATACCAGGAATCACCACCCTCACGGACTGCTT
GCGGAGGTTTACGAGGCCAGAGCACTTAGGAAGCAGTGCCAAAATCAAATGTGGTAGTTGCCAAAGCTACCAGGAATCTA
CCAAACAGCTCACAATGAATAAATTACCTGTCGTTGCCTGTTTTCATTTCAAACGGTTTGAACATTCAGCGAAACAGAGG
CGCAAGATCACTACATACATTTCCTTTCCTCTGGAGCTGGATATGACGCCGTTTATGGCCTCAAGTAAAGAGAGCAGAAT
GAATGGACAATTGCAGCTGCCAACCAATAGTGGAAACAACGAAAATAAGTATTCCTTGTTTGCTGTGGTTAATCACCAAG
GAACCTTGGAGAGTGGCCACTATACCAGCTTCATCCGGCACCACAAGGACCAGTGGTTCAAGTGTGATGATGCCGTCATC
ACTAAGGCCAGTATTAAGGACGTACTGGACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGTGCTAGAACATGAGTC
AGAAAAAGTGAAAGAAATGAACACACAAGCCTACTGA

Alignment

ORF - retro_hsap_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 75.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEQRKAWKMQGVGEKFSTWEPTKRELELLKHNPKRRKITSNCTIGLRGLINLGNTCFMNCIVQALTHTPL
          E.........G.GEKF.TWE.TK.ELELL.HNP.RR.ITS..TIGLRGLINLGNTCFMNCIVQALTHTP.
Retrocopy EVSHQQCSVPGLGEKFPTWETTKPELELLGHNPRRRRITSSFTIGLRGLINLGNTCFMNCIVQALTHTPI

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

Parental  ALDVLHRHCKGDDNGKKANNPNHCNCIIDQIFTGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFW
          ALDVLHRHCKGDD.GK.ANNPNHCNCIIDQIFTGGLQSDVTCQ.CHGVSTTIDP.WDISLDLPGS.T.FW
Retrocopy ALDVLHRHCKGDDVGKAANNPNHCNCIIDQIFTGGLQSDVTCQACHGVSTTIDPCWDISLDLPGSCTSFW

Parental  PLSPGSEGNVVNGESHVSGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHL
          P.SPG.E...VNGESH..G.TTLTDCLRRFTRPEHLGSSAKIKC..C.SYQESTKQLTM.KLP.VACFH.
Retrocopy PMSPGRESS-VNGESHIPGITTLTDCLRRFTRPEHLGSSAKIKCGSCQSYQESTKQLTMNKLPVVACFHF

Parental  KRFEHSAKLRRKITTYVSFPLELDMTPFMASSKESRMNGQYQQPTDSLNNDNKYSLFAVVNHQGTLESGH
          KRFEHSAK.RRKITTY.SFPLELDMTPFMASSKESRMNGQ.Q.PT.S.NN.NKYSLFAVVNHQGTLESGH
Retrocopy KRFEHSAKQRRKITTYISFPLELDMTPFMASSKESRMNGQLQLPTNSGNNENKYSLFAVVNHQGTLESGH

Parental  YTSFIRQHKDQWFKCDDAIITKASIKDVLDSEGYLLFYHKQFLEYE
          YTSFIR.HKDQWFKCDDA.ITKASIKDVLDSEGYLLFYHKQ.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
bodymap2_adipose	2.01 RPM	142.03 RPM
bodymap2_adrenal	3.19 RPM	120.32 RPM
bodymap2_brain	7.08 RPM	229.64 RPM
bodymap2_breast	1.36 RPM	121.64 RPM
bodymap2_colon	3.29 RPM	94.15 RPM
bodymap2_heart	1.61 RPM	115.49 RPM
bodymap2_kidney	2.92 RPM	129.67 RPM
bodymap2_liver	1.01 RPM	60.16 RPM
bodymap2_lung	1.32 RPM	103.25 RPM
bodymap2_lymph_node	1.35 RPM	121.63 RPM
bodymap2_ovary	7.25 RPM	214.32 RPM
bodymap2_prostate	3.52 RPM	100.73 RPM
bodymap2_skeletal_muscle	1.87 RPM	236.02 RPM
bodymap2_testis	2.47 RPM	107.67 RPM
bodymap2_thyroid	3.77 RPM	202.34 RPM
bodymap2_white_blood_cells	3.54 RPM	129.01 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_hsap_26 in 15 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CFW	POLR2A	X:49643847..49644366
ENCFF002CFX	POLR2A	X:49643862..49644359
ENCFF002CHO	POLR2A	X:49643960..49644397
ENCFF002CKX	POLR2A	X:49644035..49644293
ENCFF002CQC	POLR2A	X:49643757..49644237
ENCFF002CQE	POLR2A	X:49643882..49644318
ENCFF002CQK	POLR2A	X:49643912..49644402
ENCFF002CRO	POLR2A	X:49643783..49644203
ENCFF002CZD	POLR2A	X:49643721..49644231
ENCFF002DAE	POLR2A	X:49643934..49644244
ENCFF002DAH	POLR2A	X:49644049..49644333
ENCFF002DBB	POLR2A	X:49644100..49644300
ENCFF002DBO	POLR2A	X:49644118..49644245
ENCFF002DBP	POLR2A	X:49644076..49644406
ENCFF002DBQ	POLR2A	X:49644051..49644421

EST

1 EST(s) were mapped to retro_hsap_26 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW752861	49645430	49645812	99.8	381	1	380

TSS

No TSS is located nearby retro_hsap_26 retrocopy 5' end.

Lab

retro_hsap_26 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_26 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_239

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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,