RetrogeneDB ID: retro_ogar_3339

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873783.1:180561..181974(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: USP1
• Ensembl ID: ENSOGAG00000009357
• Aliases: None
• Description: ubiquitin specific peptidase 1 [Source:HGNC Symbol;Acc:12607]

Sequence

>retro_ogar_3339
ATGCCTGGTGTCATACCTAGTGAAAATAGTGGACTTTCAAGAGGTAGTCCATCTAAGAAAAGCAGACTTTCCTTAAAGTT
TTTTCAGAAAAAGGAAACTAAGAGAGCCTTGGATTTCACAGATTCTCAAGAAAATGAAGAAAAAACTTCTGAATATAGAG
GATCTGAAATTGATCAAGTTGTTCCTGCAGCACAATCCTCACCTATAAACTGTGAGAAAAGAAAAAACTTATTACCATTT
GTGGGACTGAATAATCTTGGCAATACTTGTTATCTTAATAACATACTTTAGGTACTATATTTTTGTCCCAGTTTTAAGTC
TGGAGTGAGGCACTTATTTAATATTATTTCAAGAAAGAAAGAAGCTCTAAAAGATGAAGCCAATCAGAAAGATGAGGGAA
ATTGCAAAGAAGATTCTTTGGCAAGTTATGAACTCATATGTAATCATTTAATCATGTAGTCCTTAATCACTTCAGTTGAA
CAGCTTCAGGGTAGTTTTCTCTTAAATCCAGAGAAATATACTGAAGAGCTTGCTACTCAGCCAAGGCAGCTCCTTAGTAC
ACTCAGGAAACTCAACCCTATGTATAAAGGACATCTACAGCATGATGCACAGGAAGTACTACAGTGTATTTTGGGAAATA
TTCAAGAAACATGCCAGCTCCTAAAAAAAGAAGTAAAAAATGTGGCAGAATTATCTACTACAGTGGAAGATAAACCTAAT
TAGAAAGAGGAAATGAGTGGTTTTAATGGCATGGAGACTGACAATGTTAGGCATTTTGAAGAGTGTAAAGAAAAACTCCC
TAAAGGAAATGGGGAAAGAAAAAGTGACACTGAATTTGGTAACATGAAGAAAAAAGTTAAAGTATCCAAGGAACAACAGT
CATTGGAAGAGAACCACAGACAAACCAGATCAAAAAGAAAAGCTACAAATGATACATTAGAGGTTCCTCCTAAAATAATC
CCCAAGTACATATCTGAAAAATGAGAGTACAAGACTCTCACAAAAGAAATCAAGAGTTAAGATAAATTGGTTAACGTCAG
CAACTAAGCAACCCAGCATTCTTTCTAAATTCTGTAGACTGGGAAAAATAACAACAAACCAAGGATCAAAAGGACAATCA
AAGAAAATGAGTATGATCTTGAAGAGGACTTGGGGAAGTGTGAAAGTAATAACACAGTTAATGGTTGTGGACTTGAATCT
ACAGGAAATAATGTTAAACTTGTAAATGTTAATGAAGCTAAGCCCATTAACAAAGGTACAGAGCAAATTTGTTTTGAGCT
AGTGGAGAAATTATTTCAAGGTCAGCTGGTGTTAAGAACTCATTGCTTGGAATGTGAAAGTTTAACCAAAAGAAGAGAAG
ATTTTAAAGACATTAGTGTGCCAGTGCAAGAAGCTTTCCAAAGTAGAGGAGAG

Alignment

ORF - retro_ogar_3339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 59.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPGVIPSENNGLSRGSPSKKNRLSLKFFQKKETKRALDFTDSQENEEKASEYRGSEIDQVVPAAQSSPLN
          MPGVIPSEN.GLSRGSPSKK.RLSLKFFQKKETKRALDFTDSQENEEK.SEYRGSEIDQVVPAAQSSP.N
Retrocopy MPGVIPSENSGLSRGSPSKKSRLSLKFFQKKETKRALDFTDSQENEEKTSEYRGSEIDQVVPAAQSSPIN

Parental  CEKRENLLPFVGLNNLGNTCYLNSILQVLYFCPGFKSGVKHLFNIISRKKEALKDEANQKDKGNCKEDSL
          CEKR.NLLPFVGLNNLGNTCYLN.IL.VLYFCP.FKSGV.HLFNIISRKKEALKDEANQKD.GNCKEDSL
Retrocopy CEKRKNLLPFVGLNNLGNTCYLNNIL*VLYFCPSFKSGVRHLFNIISRKKEALKDEANQKDEGNCKEDSL

Parental  ASYELICS---LQSLIISVEQLQASFLLNPEKYTEELATQPRRLLNTLRELNPMYEGYLQHDAQEVLQCI
          ASYELIC......SLI.SVEQLQ.SFLLNPEKYTEELATQPR.LL.TLR.LNPMY.G.LQHDAQEVLQCI
Retrocopy ASYELICNHLIM*SLITSVEQLQGSFLLNPEKYTEELATQPRQLLSTLRKLNPMYKGHLQHDAQEVLQCI

Parental  LGNIQETCQLLKKEEVKNVAELSTKVEENPNQKEEMSGFNGMETDNVRHFEECKEKLPKGNGKRKSDIEF
          LGNIQETCQ.L.......VAELST.VE..PN.KEEMSGFNGMETDNVRHFEECKEKLPKGNG.RKSD.EF
Retrocopy LGNIQETCQ-LXXXXXXXVAELSTTVEDKPN*KEEMSGFNGMETDNVRHFEECKEKLPKGNGERKSDTEF

Parental  GNMKKKVKVSKEQQSLEENHRQTRSKRKATDDTLEVPPKIIPKYISE-NESTRLSQKKSRVKINWFKSAT
          GNMKKKVKVSKEQQSLEENHRQTRSKRKAT.DTLEVPPKIIPKYISE.NESTRLSQKKSRVKINW..SAT
Retrocopy GNMKKKVKVSKEQQSLEENHRQTRSKRKATNDTLEVPPKIIPKYISE>NESTRLSQKKSRVKINWLTSAT

Parental  KQPSILSKFCSLGKITTSQGSKGQS-KEDEYDLEEDLGKCESTNTVNGCGLESTGNDVKPVDVNEAKPIN
          KQPSILSKFC.LGKITT.QGSKGQS.KE.EYDLEEDLGKCES.NTVNGCGLESTGN.VK.V.VNEAKPIN
Retrocopy KQPSILSKFCRLGKITTNQGSKGQS<KENEYDLEEDLGKCESNNTVNGCGLESTGNNVKLVNVNEAKPIN

Parental  KGTEQIGFELVEKLFQGQLVLRTRCLECESLTERREDFQDISVPVQEDELSKVE
          KGTEQI.FELVEKLFQGQLVLRT.CLECESLT.RREDF.DISVPVQE...S..E
Retrocopy KGTEQICFELVEKLFQGQLVLRTHCLECESLTKRREDFKDISVPVQEAFQSRGE

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_3339 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012439	1 retrocopy	retro_mluc_1727,
Mus musculus	ENSMUSG00000028560	1 retrocopy	retro_mmus_2136,
Otolemur garnettii	ENSOGAG00000009357	1 retrocopy	retro_ogar_3339 ,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Tursiops truncatus	ENSTTRG00000013871	1 retrocopy	retro_ttru_554,