RetrogeneDB ID: retro_ptro_3168

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:129035096..129035953(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUVBL2
• Ensembl ID: ENSPTRG00000011270
• Aliases: None
• Description: None

Sequence

>retro_ptro_3168
ATGGCAACTGTGATGACCGTGACCAATGTTCCAGAGATCTATGATGTGAGGAGAACTGAGCATAGAGGTGTTCACTCCCA
CATCTGAGGACTGGGGCTGGATGATGCTTTGGAGGCTCAACAGGCTTCCCAGGGCATGGTGGGTCAGCTTTGCTGCACAG
CAGGCAGCTCGTGTGGGGCTGGAGATGATCCATAAAGGGAAGATTGTCAAGTGGGCAGTCCTCATTGCTGGTCAGCTGGG
CAGAGGGAAGACAGCCATCGCCCTAGACATGGCATAGGCCCTGGGACCTGACACCTTGTTCATAGCCATCACCGGCAGTG
AGATCTCCCTGGAGATGAGCAAGACCCAGGCACTGACACAGGCTTTCTGGCCATCTTTTGGCATTCACTTCAAGGAGGAG
ATGGAGATCATCGAAGGGGAAGTGGTTGAGACCCAGATTTATAGAACAGTGACAGGAATGGGCTCCAAGGTGGGCAAACT
GACTAACAAAACCAAGAAGATGGAGACCATCTATGACCTGGGCATGAAGATGATTGAGTCCCTGACCAAAGACAAGATCC
ACGCTGGTGACATGATCACTATTGACAAAGCAATGGGAAAGATCTCCAAGTTGGGCCACTCCTTTACATGGTCTGGTGAC
TACAACCCCATGGACTCCCAGACCAAATTCAGGCAGCCCCCATATGGGAAGCTCCAGAAATGCAAGGCGCATACTGTGTC
CCTTGCACAAGATCAACATCATCAACTCCCACACGCATGGCTTCCTGGCTCTCTTCTCATGTGACACAAGAGAGATCAAG
TCAGAAGTTGCCAAGCAGATCAATGTCAAAGTGGCCGAGTGGATGGAACAAAATAGA

Alignment

ORF - retro_ptro_3168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.38 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQL-AARRAAGVVLEMIREGKIA
          MATV...T.VPEI.DV.R.E..G.HSHI.GLGLDDALE..QASQGMVGQL.AA..AA.V.LEMI..GKI.
Retrocopy MATVMTVTNVPEIYDVRRTEHRGVHSHI*GLGLDDALEAQQASQGMVGQL>AAQQAARVGLEMIHKGKIV

Parental  GRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE
          ..AVLIAGQ.G.GKTAIA..MA.ALGPDT.F.AI.GSEI.SLEMSKT.ALTQAF..S.G...KEE.EIIE
Retrocopy KWAVLIAGQLGRGKTAIALDMA*ALGPDTLFIAITGSEI-SLEMSKTQALTQAFWPSFGIHFKEEMEIIE

Parental  GEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSF
          GEVVE.QI.R..TG.GSKVGKLT.KT..METIYDLG.KMIESLTKDK..AGD.ITIDKA.GKISKLG.SF
Retrocopy GEVVETQIYRTVTGMGSKVGKLTNKTKKMETIYDLGMKMIESLTKDKIHAGDMITIDKAMGKISKLGHSF

Parental  TRARDYDAMGSQTKFVQCPDGELQKRKEVVHTVS-LHEIDVINSRTQGFLALFSGDTGEIKSEVREQINA
          T...DY..M.SQTKF.Q.P.G.LQK.K...HTVS.LH.I..INS.T.GFLALFS.DT.EIKSEV..QIN.
Retrocopy TWSGDYNPMDSQTKFRQPPYGKLQKCK--AHTVS>LHKINIINSHTHGFLALFSCDTREIKSEVAKQINV

Parental  KVAEWREEGK
          KVAEW.E...
Retrocopy KVAEWMEQNR

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	31.53 RPM
SRP007412_cerebellum	0.00 RPM	26.85 RPM
SRP007412_heart	0.00 RPM	9.53 RPM
SRP007412_kidney	0.00 RPM	35.67 RPM
SRP007412_liver	0.00 RPM	32.47 RPM
SRP007412_testis	0.00 RPM	197.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3168 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3168 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3168 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4755
Gorilla gorilla	retro_ggor_2961
Pongo abelii	retro_pabe_3701
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 ,