RetrogeneDB ID: retro_pabe_3814

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:134977252..134978010(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR4
• Ensembl ID: ENSPPYG00000011458
• Aliases: None
• Description: WD repeat domain 4 [Source:HGNC Symbol;Acc:12756]

Sequence

>retro_pabe_3814
GCCACCTCTGCTGCAAACAATGATGACAACAACCTCTTCATCTATGACTGCAGTGCTGCAGAATAGTCACAAGAAAATAA
AGGGGAGGATGGGCTACCCTTGGTCTGGGGGAGTGGCATGATTCTGGCATCCACCTCCAAGTCTGGCAGCTATTTTGCTT
TAACAGATGACCACAAGCGTCTGATTCTTTTCCATACAAAACCATGGCAATGTCTGAGTGTCAGGACCATGGCAAGGAGG
TGTATGGCCCTGACCTTACAGCCTCTGTGGAGAAGGTCTTGGTGGCCGACAAATCTGGAGATGTGTACTCCTTTTTGGTT
TCAGAGCCACACAGATGCGGCAGACTTGACCTGGCACACCTGTCAATGTTGTTAGAGGTGACTGTGAGTGCTGATAACTG
CTTCATCCTCATTGCCAACCAGGATGAGAAGATCCAGGTCAGCTAGGCCACAGCACCTCACAGTATCGAGTCCTTCTGCC
TCGGGCACAGAGAATTCGTGAGCCGCATCTCTGTGGTGCCCACTCAGCCCGAACTGTTTCTTGTCCTCCTCCAGGGACTG
CACTCTTAGGCTCTAGGAGTACAGAAGTGGCCATCAACTGCACTTCTGTCACCTGGCCAGTCTGCAAGGGCTGATGGGCC
TCTGGGACACCAGAAGTTTGTCACATCCGGGATCACGTTCTGGTGCTAGGAGAACTGCATGACGCTTCTGTGCAACTGTA
TTCCCGTAATCTACATCTTCCAGCTTGATGCTCTCAGA

Alignment

ORF - retro_pabe_3814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.19 %
• Parental protein coverage: 61.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ATSTASSDDDSLFIYDCSAAEKKSQENKGEDA-PLDQGSGAILASTFSKSGSYFALTDDSKRLILFRTKP
          ATS.A..DD..LFIYDCSAAE..SQENKGED..PL..GSG.ILAST.SKSGSYFALTDD.KRLILF.TKP
Retrocopy ATSAANNDDNNLFIYDCSAAE*-SQENKGEDGLPLVWGSGMILAST-SKSGSYFALTDDHKRLILFHTKP

Parental  WQCLSVRTVARRCTALTF-TASEEKVLVADKSGDVYSFSVLEPHRCGRLELGHLSMLLDVAVSPDDCFIL
          WQCLSVRT.ARRC.ALT..TAS.EKVLVADKSGDVYSF.V.EPHRCGRL.L.HLSMLL.V.VS.D.CFIL
Retrocopy WQCLSVRTMARRCMALTL<TASVEKVLVADKSGDVYSFLVSEPHRCGRLDLAHLSMLLEVTVSADNCFIL

Parental  TADRDEKIRVSWAAAPHSIESFCLGHTEFVSRISLVPTQPGL-LLSSSGDGTLRLWEYRSGRQLHCCHLA
          .A..DEKI.VS.A.APHSIESFCLGH.EFVSRIS.VPTQP.L..LSSS.D.TLRL.EYRSG.QLH.CHLA
Retrocopy IANQDEKIQVS*ATAPHSIESFCLGHREFVSRISVVPTQPEL>FLSSSRDCTLRL*EYRSGHQLHFCHLA

Parental  SLQELV-DPQAPQRFAASRIAFWCQENCVALLCDGTPVVYIFQLDAHR
          SLQ.L...P...Q.F..S.I.FWC.ENC..LLC...PV.YIFQLDA.R
Retrocopy SLQGLM<GPLGHQKFVTSGITFWC*ENCMTLLCNCIPVIYIFQLDALR

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	3.04 RPM
SRP007412_cerebellum	0.00 RPM	1.46 RPM
SRP007412_heart	0.00 RPM	0.69 RPM
SRP007412_kidney	0.00 RPM	3.45 RPM
SRP007412_liver	0.00 RPM	1.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3814 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3814 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4905
Gorilla gorilla	retro_ggor_3063

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160193	1 retrocopy	retro_hsap_4905,
Gorilla gorilla	ENSGGOG00000016652	1 retrocopy	retro_ggor_3063,
Nomascus leucogenys	ENSNLEG00000014641	1 retrocopy	retro_nleu_2350,
Pongo abelii	ENSPPYG00000011458	1 retrocopy	retro_pabe_3814 ,