RetrogeneDB ID: retro_ptro_934

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:69436297..69436891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP25
• Ensembl ID: ENSPTRG00000019495
• Aliases: None
• Description: Sin3A-associated protein, 25kDa [Source:HGNC Symbol;Acc:41908]

Sequence

>retro_ptro_934
ATGACTCCACTAGCGCCCTGGGACCCCAAGTACGAAGCCAAAGCAGGACCTCGGCTGGTGTGGGGGCCAACTGTAGCTCA
GGAGCCTCGTTCTCAGGCCGGACGGTGTGTCACCCCTCGTTCTGGCCGCTGTACGAGGCAGCCTCGGGCAGGGGTCTCAG
GCCCGTGGCCCCTGCCACAGGGCATTGGAATGGACAGCGGGCGCCCCCGGATGCAGGGTTCCCGGTGATGTGCTGTGAAG
ACGTCTTCCTCTCGGACCCTCTGCTGCCCCGGGGGCAGAGTGTCCCCCTGTACCTGTCCAAGGCCCCCCAGCAGATGATG
GGCTCCCTGAAACTGCTGCCGCCGCCCCCCATCATGTCTGCCAAGGTTCTCCCCCGCCTGTCCCTCCCTGGGCCCCTCCA
CGGCCTGGCTCAGCGGGCCGGAGCTGATCGCTCTCACTGGCCGGCTGCAGGTGAGCCAGGGGGAGCCTAGGCCCAGCTCC
TCCGCGGCTGGCCCCCCAGACCCTACCTCTGACCCACCCAGCCCCAGTGGTAGCCCCAGCAGTTTTCAGAGTGCTGACCT
CTCTCTCCCACAGACCCCAGACACCCATTGTCCA

Alignment

ORF - retro_ptro_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTPLAPWDPKYEAKAGPRPVWG-ANCSSGASFSGRTLCHPSFWPLYEAASGRGLRPVAPATGHWNGQQAP
          MTPLAPWDPKYEAKAGPR.VWG.ANCSSGASFSGRT.CHPSFWPLYEAASGRGLRPVAPATGHWNGQ.AP
Retrocopy MTPLAPWDPKYEAKAGPRLVWG<ANCSSGASFSGRTVCHPSFWPLYEAASGRGLRPVAPATGHWNGQRAP

Parental  PDAGFPVVCCEDVFLSDPLLPRGQRVPLYLSKAPQQMMGSLKLLPPPPIMSARVLPR-PSP-SRGPSTAW
          PDAGFPV.CCEDVFLSDPLLPRGQ.VPLYLSKAPQQMMGSLKLLPPPPIMSA.VLPR.P.P.S.GPSTAW
Retrocopy PDAGFPVMCCEDVFLSDPLLPRGQSVPLYLSKAPQQMMGSLKLLPPPPIMSAKVLPR<PVP<SLGPSTAW

Parental  LSGPELIALTGLLQMSQGEPRPSSSAVGPPDHTSDPPSPCGSPSSSQGADLSLPQTPDTHCP
          LSGPELIALTG.LQ.SQGEPRPSSSA.GPPD.TSDPPSP.GSPSS.Q.ADLSLPQTPDTHCP
Retrocopy LSGPELIALTGRLQVSQGEPRPSSSAAGPPDPTSDPPSPSGSPSSFQSADLSLPQTPDTHCP

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	0.04 RPM	2.63 RPM
SRP007412_cerebellum	0.04 RPM	1.97 RPM
SRP007412_heart	0.00 RPM	0.44 RPM
SRP007412_kidney	0.00 RPM	3.82 RPM
SRP007412_liver	0.00 RPM	2.52 RPM
SRP007412_testis	0.11 RPM	2.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_934 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_934 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1362
Gorilla gorilla	retro_ggor_1060

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015273	1 retrocopy	retro_cjac_1085,
Homo sapiens	ENSG00000205307	1 retrocopy	retro_hsap_1362,
Gorilla gorilla	ENSGGOG00000013708	1 retrocopy	retro_ggor_1060,
Pongo abelii	ENSPPYG00000017415	1 retrocopy	retro_pabe_1129,
Pan troglodytes	ENSPTRG00000019495	1 retrocopy	retro_ptro_934 ,