RetrogeneDB ID: retro_pabe_3701

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:127863295..127863972(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUVBL2
• Ensembl ID: ENSPPYG00000010225
• Aliases: None
• Description: RuvB-like 2 (E. coli) [Source:HGNC Symbol;Acc:10475]

Sequence

>retro_pabe_3701
ATGGTGGGTCAGCTTTGCTGCACAGCAGGCAGCTGATGTGGGGCGGGAGATGATCCATAAGGGGAAGATTGTCAAGTGGG
CAGTCCTCATTGCTGGTCAGCTGGGCAGAGGGAAGACAGCCATCGCCCTAGGCATGGCATAGGCCCTGGGACCTGACACC
TTGTTCATAGCCATCACCGGCAGTGAGATCTCCCTGGAGATGAGCAAGACCCAGGCTTTCTGGCCATCTTTTGGCATTCA
CTTCAAGGAGGAGATGGAGATCATCGAAGGGGAAGTGGTTGAGACCCAGATTGATAGACCAGTGACAGGAATGGGCTCCA
AGGTGGGCAAACTGACCATCAAAACCAAGAAGATGGAGACCATCTATGACCTGGGCATGAAGATGATTGAGTCCCTGACC
AAAGACAAGATCCACGCTGGTGACATGATCACTATTGACAAAGCAATGGGCAAGATCTCCAAGTTGGGCCACTCCTTTAC
ATGGTCCGGTGACTACAACCCCATGGACTCCCAGACTAAATTCGGGCAGACCCCATATGGGAAGCTCCAGAAATGCAAGG
TGCACATTGTGTCCCTTGCACAAGATCGACATCATCAACTCCCACACCCATGTCTTCCTGGCTCTCTTCTCATGTGACAC
AGAGAGATCAGTCGAAGTTGCCAAGCAGATCACGTCA

Alignment

ORF - retro_pabe_3701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.79 %
• Parental protein coverage: 55.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVGQL-AARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMS
          MVGQL.AA..AA.V..EMI..GKI...AVLIAGQ.G.GKTAIA.GMA.ALGPDT.F.AI.GSEI.SLEMS
Retrocopy MVGQL>AAQQAADVGREMIHKGKIVKWAVLIAGQLGRGKTAIALGMA*ALGPDTLFIAITGSEI-SLEMS

Parental  KTEALTQAFRRSIGVRIKEETEIIEGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTK
          K....TQAF..S.G...KEE.EIIEGEVVE.QIDRP.TG.GSKVGKLT.KT..METIYDLG.KMIESLTK
Retrocopy K----TQAFWPSFGIHFKEEMEIIEGEVVETQIDRPVTGMGSKVGKLTIKTKKMETIYDLGMKMIESLTK

Parental  DKVQAGDVITIDKATGKISKLGRSFTRARDYDAMGSQTKFVQCPDGELQKRKEVVHTVS-LHEIDVINSR
          DK..AGD.ITIDKA.GKISKLG.SFT...DY..M.SQTKF.Q.P.G.LQK.K..VH.VS.LH.ID.INS.
Retrocopy DKIHAGDMITIDKAMGKISKLGHSFTWSGDYNPMDSQTKFGQTPYGKLQKCK--VHIVS>LHKIDIINSH

Parental  TQGFLALFSGDTGEIKSEVREQINA
          T..FLALFS.DT.E...EV..QI..
Retrocopy THVFLALFSCDT-ERSVEVAKQITS

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_prefrontal_cortex	0.00 RPM	34.39 RPM
SRP007412_cerebellum	0.00 RPM	21.04 RPM
SRP007412_heart	0.00 RPM	12.94 RPM
SRP007412_kidney	0.00 RPM	36.63 RPM
SRP007412_liver	0.00 RPM	23.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3701 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3701 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4755
Pan troglodytes	retro_ptro_3168
Gorilla gorilla	retro_ggor_2961
Macaca mulatta	retro_mmul_2536

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000222	2 retrocopies	retro_cjac_329, retro_cjac_4119,
Homo sapiens	ENSG00000183207	1 retrocopy	retro_hsap_4755,
Gorilla gorilla	ENSGGOG00000009245	1 retrocopy	retro_ggor_2961,
Macropus eugenii	ENSMEUG00000000069	1 retrocopy	retro_meug_2099,
Macaca mulatta	ENSMMUG00000003915	1 retrocopy	retro_mmul_2536,
Nomascus leucogenys	ENSNLEG00000004769	1 retrocopy	retro_nleu_1251,
Otolemur garnettii	ENSOGAG00000007519	2 retrocopies	retro_ogar_2473, retro_ogar_3246,
Pongo abelii	ENSPPYG00000010225	1 retrocopy	retro_pabe_3701 ,
Pan troglodytes	ENSPTRG00000011270	1 retrocopy	retro_ptro_3168,