RetrogeneDB ID: retro_ogar_274

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:3429413..3431021(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000028141
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: USP22
• Ensembl ID: ENSOGAG00000015801
• Aliases: None
• Description: ubiquitin specific peptidase 22 [Source:HGNC Symbol;Acc:12621]

Sequence

>retro_ogar_274
GTGGGGCCACCAGGTTGCTCCCACGTGAACAGCTTTAAGGTGGGAGAGAACTGGAGGCAGGAACTGCGGGTCATCTACCA
GTGCTTCGTGTGGTGTGGAACCCCAGAGACCAGGAAAAGCAAAGCAAAGTCGTGCATCTGCCATGTGTGTGGCACCCATT
TGAACAGACTCCACTCTTGCCTTTTCTGTGTCTTCTTTGGCTGCTTCACAGAGAAACACATTCACGAGCACGCTGAGACA
AAACAACACAACTTAGCCGTAGACCTTTATTATGGAGGTATATACTGCTTTATGTGTAAGGACTATGTTTATGACAAAGA
CATTGAGCAAATTGCCAAAGAAGAGCAAGGAGAGGCTTTGAAATTACAAGCCTCCACCTCAACAGAGCTATCTCACCAGC
AGTGTTCAGTGCCAGGCATTGGTGAGAAATACCCAACCTGGGAAACAACCAAACCGGAATTGGAACTCCTGGGGCACAAC
CCCAGGAGAAGGAGAATCACCTCCAGCTTCACCATCGGTTTAAGAGGACTAATCAATCTTGGCAACACGTGCTTTATGAA
CTGCATTGTCCAGGCCCTTACGCACACACCAATACTGAGAGATTTCTTCCTCTCTGATAGGCACCGATGTGAAATGCCGA
GTCCTGAGTTGTGCCTGGTCTGTGAGATGTCTTCACTCTTTAGGGAGTTGTATTCTGGAAACCCATCTCCTCATGTTCCT
TATAAGTTACTGCACCTGGTGTGGATACATGCTCGCCATTTAGCAGGGTACAGGCAACAGGATGCCCATGAGTTCCTCAT
TGCGGCGTTAGATGTCCTGCACAGGCACTGCAAAGGTGACGATGTCGGAAAGGCAGCCAATAATCCCAACCACTGTAATT
GCATCATAGACCAAATCTTTACAGGTGGCCTGCAGTCCGATGTCACCTGTCAAGCCTGCCATGGTGTTTCCACTACCATA
GATCCATGCTGGGACATTAGTTTGGACTTGCCTGGCTCTTGCACCTCCTTCTGGCCCATGAGCCCAGGGAGGGAGAGCAG
TGTGAATGGAGAAAGCCACATATCTGGGATCACCACCCTCACGGACTGCTTGCGGAGGTTTACGAGACCAGAGCACTTAG
GAAGCAGTGCCAAAATCAAATGTGGTAGTTGCCAAAGCTACCAGGAATCTACCAAACAGCTCACGATGAATAAATTACCT
GTTGTTGCCTGTTTTCATTTCAAACGCTTTGAACACTCAGCCAAACAGAGGCGCAAGATCACTACATACATTTCCTTTCC
TCTGGAGTTGGATATGACACCGTTTATGGCCTCAAGTAAAGAGAGCAGAATGAATGGACAGTTGCAGCTGCCAACCAATA
GTGGAAACAACGAGAATAAGTATTCCTTGTTTGCTGTGGTTAATCACCAAGGAACTTTGGAGAGTGGCCACTATACCAGC
TTCATCCGGCATCACAAGGACCAGTGGTTCAAGTGTGATGATGCCGTCATCACCAAGGCCAGTATTAAGGATGTACTGGA
CAGTGAAGGGTATTTACTGTTCTATCACAAACAGGTCCTGGAACATGAGTCAGAAAAAGTGAAAGAAATGAATACACAAG
CCTACTGA

Alignment

ORF - retro_ogar_274 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 84.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAPPGCSHLSSFKV-DNWKQNLRAIYQCFVWSGTAEARKRKAKSCVCHVCGVHLNRLHSCLYCVFFGCFT
          V.PPGCSH..SFKV..NW.Q.LR.IYQCFVW.GT.E.RK.KAKSC.CHVCG.HLNRLHSCL.CVFFGCFT
Retrocopy VGPPGCSHVNSFKVGENWRQELRVIYQCFVWCGTPETRKSKAKSCICHVCGTHLNRLHSCLFCVFFGCFT

Parental  KKHIHEHAKSKRHNLAIDLMYGGIYCFLCQDYIYDKDMEIIAKEEQRKAWKLQESDLSTAAKQQQWLQPR
          .KHIHEHA..K.HNLA.DL.YGGIYCF.C.DY.YDKD.E.IAKEEQ..A.KLQ.S..ST....QQ...P.
Retrocopy EKHIHEHAETKQHNLAVDLYYGGIYCFMCKDYVYDKDIEQIAKEEQGEALKLQAST-STELSHQQCSVPG

Parental  VGEKFSTWEPTKRELELLKHNPKRRKITANCTIGLRGLINLGNTCFMNCIVQALTHTPLLRDFFLSDRHR
          .GEK..TWE.TK.ELELL.HNP.RR.IT...TIGLRGLINLGNTCFMNCIVQALTHTP.LRDFFLSDRHR
Retrocopy IGEKYPTWETTKPELELLGHNPRRRRITSSFTIGLRGLINLGNTCFMNCIVQALTHTPILRDFFLSDRHR

Parental  CEMQSPSSCLVCEMSSLFQEFYSGHRSPHIPYKLLHLVWTHARHLAGYEQQDAHEFLIAALDVLHRHCKG
          CEM.SP..CLVCEMSSLF.E.YSG..SPH.PYKLLHLVW.HARHLAGY.QQDAHEFLIAALDVLHRHCKG
Retrocopy CEMPSPELCLVCEMSSLFRELYSGNPSPHVPYKLLHLVWIHARHLAGYRQQDAHEFLIAALDVLHRHCKG

Parental  DDNGKKANNPNHCNCIIDQIFTGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFWPLSPGSEGSVV
          DD.GK.ANNPNHCNCIIDQIFTGGLQSDVTCQ.CHGVSTTIDP.WDISLDLPGS.T.FWP.SPG.E.S.V
Retrocopy DDVGKAANNPNHCNCIIDQIFTGGLQSDVTCQACHGVSTTIDPCWDISLDLPGSCTSFWPMSPGRESS-V

Parental  NGESHVSGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHLKRFEHSAKLRR
          NGESH.SG.TTLTDCLRRFTRPEHLGSSAKIKC..C.SYQESTKQLTM.KLP.VACFH.KRFEHSAK.RR
Retrocopy NGESHISGITTLTDCLRRFTRPEHLGSSAKIKCGSCQSYQESTKQLTMNKLPVVACFHFKRFEHSAKQRR

Parental  KITTYVSFPLELDMTPFMASSKESRMNGQYQQPVDSLSSDNKYSLFAVVNHQGTLESGHYTSFIRQHKDQ
          KITTY.SFPLELDMTPFMASSKESRMNGQ.Q.P..S....NKYSLFAVVNHQGTLESGHYTSFIR.HKDQ
Retrocopy KITTYISFPLELDMTPFMASSKESRMNGQLQLPTNSGNNENKYSLFAVVNHQGTLESGHYTSFIRHHKDQ

Parental  WFKCDDAIITKASIKDVLDSEGYLLFYHKQFLEYE
          WFKCDDA.ITKASIKDVLDSEGYLLFYHKQ.LE.E
Retrocopy WFKCDDAVITKASIKDVLDSEGYLLFYHKQVLEHE

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_274 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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,