RetrogeneDB ID: retro_ptro_2698

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:71617848..71618616(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VENTX
• Ensembl ID: ENSPTRG00000003087
• Aliases: None
• Description: VENT homeobox [Source:HGNC Symbol;Acc:13639]

Sequence

>retro_ptro_2698
ATGCGTCCCTCTTCCTCCCCACCTTGCGGCCGGCAGCAGCCCTCTAGCTTTGGCTCCGTGGACTGGCTCTCCCAAAGCAG
CTGCTCAGGGCCGACCCACACCCCCAGGCCTGCCGAGGTCTCCCTGGGGAGCCTCCCTGGCCCGGACCAGGCATCTGGCC
CCGAGGAGCCCCCTCAGGCCGTCAGCATCAAGGAGGCTAGGTCCTCAAATCTGCCTCCACCAGAGAGGGCTATGGCTGGG
TTGAGGAAAGGGCCAAACGCCTGGCGGGCCCCACTGTGTCCACACAGCCTTCACCACGGAGCAGGTCCGTGGCTTGGAGG
GCATCTTCCGGCACCACCAGTACCTGGGCCCTCTGGAGTGGAAGAGGCTGGCCAGGGAAATGCAGCTGTCGGAGGTCCAG
ATAAAAACCTGGTTTCAAAATCGCCGCATAAAACACGAGCGGCAAATGCAGGACTCCCAGCTGAACAGCCCCTTCTCGGA
GTCACTGCACGCACCCCTGGCTTTCCACTCACCGTCTTCTGGCCTTGCCAATGGCCTGCACCTGCTGTGCCCTTGGGCAC
CCCTGCCTGGGCCCCAGACTCTGATGCTGTCCCCTGGCTCCTGAGGTCTCTGCCAAGTGGAACAAGAGGCCCTGGCCTCT
GAGTGGGCCTCCTGCTGTGGGCAGACTCTGGCATACCACCCCCCAAAGCCCAGGAAGTGGCATGCATACGCTGGGACCAG
CCCTGTCCACGGGGCCCTGGGGCCTGGTGTGCTCTGCCGGAGACGGGA

Alignment

ORF - retro_ptro_2698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.08 %
• Parental protein coverage: 98.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRLSSSPPRGRQQLSSFGSVDWLSQSSCSGPTHTPRPADFSLGSLPGPGQTSGAREPPQAVSIKEAARSS
          MR.SSSPP.GRQQ.SSFGSVDWLSQSSCSGPTHTPRPA..SLGSLPGP.Q.SG..EPPQAVSIKEA.RSS
Retrocopy MRPSSSPPCGRQQPSSFGSVDWLSQSSCSGPTHTPRPAEVSLGSLPGPDQASGPEEPPQAVSIKEA-RSS

Parental  NLPAPERTVAGLSKEPNTLRVPR-VRTAFTMEQVRTLEGVFQHHQYLSPLERKRLAREMQLSEVQIKTWF
          NLP.PER..AGL.K.PN..R.P..V.TAFT.EQVR.LEG.F.HHQYL.PLE.KRLAREMQLSEVQIKTWF
Retrocopy NLPPPERAMAGLRKGPNAWRAPL>VHTAFTTEQVRGLEGIFRHHQYLGPLEWKRLAREMQLSEVQIKTWF

Parental  QNRRMKHKRQMQDPQLHSPFSGSLPAPPAFYSPSSGLANGLQLLCPWAPLSGPQALMLPPGSFWGLCQVA
          QNRR.KH.RQMQD.QL.SPFS.SL.AP.AF.SPSSGLANGL.LLCPWAPL.GPQ.LML.PGS..GLCQV.
Retrocopy QNRRIKHERQMQDSQLNSPFSESLHAPLAFHSPSSGLANGLHLLCPWAPLPGPQTLMLSPGS*-GLCQVE

Parental  QEALASVGASCCGQPLASH-PPTPGRP--TLGPALSTGPRGL-CAMPQTG
          QEALAS..ASCCGQ.LA.H.P..PG....TLGPALSTGP.GL.CA.P.TG
Retrocopy QEALASEWASCCGQTLAYH>PQSPGSGMHTLGPALSTGPWGL>CALPETG

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	0.07 RPM	0.00 RPM
SRP007412_cerebellum	0.29 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.05 RPM	0.00 RPM
SRP007412_liver	0.10 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2698 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2698 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3973
Macaca mulatta	retro_mmul_2294

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151650	4 retrocopies	retro_hsap_1027, retro_hsap_2612, retro_hsap_3973, retro_hsap_4038,
Gorilla gorilla	ENSGGOG00000003340	3 retrocopies	retro_ggor_1830, retro_ggor_2668, retro_ggor_2708,
Macaca mulatta	ENSMMUG00000000543	2 retrocopies	retro_mmul_1477, retro_mmul_2294,
Nomascus leucogenys	ENSNLEG00000002047	5 retrocopies	retro_nleu_2033, retro_nleu_2054, retro_nleu_635, retro_nleu_664, retro_nleu_905,
Pan troglodytes	ENSPTRG00000003087	4 retrocopies	retro_ptro_1761, retro_ptro_2698 , retro_ptro_2736, retro_ptro_702,