RetrogeneDB ID: retro_pvam_905

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_15965:20287..21166(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000009297
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: USP22
• Ensembl ID: ENSPVAG00000001934
• Aliases: None
• Description: ubiquitin specific peptidase 22 [Source:HGNC Symbol;Acc:12621]

Sequence

>retro_pvam_905
TACTCTGGAAGCCGAACTCCTCACATTCCCTATAAGTTACTGCACCTGATATGGATTCATGCAGAACACTTAGCGGGGTA
CAGGCAGCAGGATGCCCATGAGTTCCTTATTGCCATATTAGATGTACTGCATAGACACAGCAAAGATGATAGTGTTGGGC
AGGAAGCCAGTAACCCCAACGGCTGTAACTGCATTATAGACCAAATCTTTACAGGTGGCTTGCAGTCTGATGTCACATGT
CAGGCTTGCCATAGCGTGTCCACAACAATAGACCCGTGTTGGGACATCAGTTTGGATTTGCCTGGCTCTTATGCCACATT
CAGTTCTCAGAGTCCAGAGAGGCCTGACAGCACAGTGCATAGGGATGACTACATGCCAGGAATCCCCTCTCTCACAGACT
GCCTCCAATGGTTTACAAGGCCAGAGCACCTGGGAAGCAGTGCCAAAATCAAATGCAGTAGTTGCCAAAGCTACCAGGAA
TCTACCAAACAGCTCACAATGAAGAAGTTACCCATTGTGGCCTGTTTTCATCTAAAGCGGTTTGAACATTTAGGCAAACA
GAGACGAAAAATTAATACTTTTATCTCCTTTCCTTTGGAGCTGGACATGACTCCATTTTTGGCCTCCACTAAAGAGAATG
GAATGAAAGATGACCAGCCACAAACTGATTGTGCGCCCAATGAGAATAAGTATTCCTTGTTTGCAGTGATTAACCACCAT
GGAACTTTGGAAAGTGGACACTACACCAGCTTTATCCGACAACAAAAGGACCAGTGGTTCAGCTGTGATGATGCCGTCAT
CACCAAGGCTACCATTGAGGACTTACTCTACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGGTCTAGAGAAAGAG

Alignment

ORF - retro_pvam_905 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.83 %
• Parental protein coverage: 56.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YSGHRSPHIPYKLLHLVWTHARHLAGYEQQDAHEFLIAALDVLHRHCKGDDNGKKANNPNHCNCIIDQIF
          YSG.R.PHIPYKLLHL.W.HA.HLAGY.QQDAHEFLIA.LDVLHRH.K.D..G..A.NPN.CNCIIDQIF
Retrocopy YSGSRTPHIPYKLLHLIWIHAEHLAGYRQQDAHEFLIAILDVLHRHSKDDSVGQEASNPNGCNCIIDQIF

Parental  TGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFWPLSPGSEGSVVNGESHVSGTTTLTDCLRRFTR
          TGGLQSDVTCQ.CH.VSTTIDP.WDISLDLPGS...F...SP....S.V.......G...LTDCL..FTR
Retrocopy TGGLQSDVTCQACHSVSTTIDPCWDISLDLPGSYATFSSQSPERPDSTVHRDDYMPGIPSLTDCLQWFTR

Parental  PEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHLKRFEHSAKLRRKITTYVSFPLELDMTPFMASS
          PEHLGSSAKIKCS.C.SYQESTKQLTMKKLPIVACFHLKRFEH..K.RRKI.T..SFPLELDMTPF.AS.
Retrocopy PEHLGSSAKIKCSSCQSYQESTKQLTMKKLPIVACFHLKRFEHLGKQRRKINTFISFPLELDMTPFLAST

Parental  KESRMNGQYQQPADSLNNDNKYSLFAVVNHQGTLESGHYTSFIRQHKDQWFKCDDAIITKASIEDVLDSE
          KE..M....Q...D...N.NKYSLFAV.NH.GTLESGHYTSFIRQ.KDQWF.CDDA.ITKA.IED.L.SE
Retrocopy KENGMKDD-QPQTDCAPNENKYSLFAVINHHGTLESGHYTSFIRQQKDQWFSCDDAVITKATIEDLLYSE

Parental  GYLLFYHKQFLEYE
          GYLLFYHKQ.LE.E
Retrocopy GYLLFYHKQGLEKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_905 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,