RetrogeneDB ID: retro_pabe_1129

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:71292497..71293220(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP25
• Ensembl ID: ENSPPYG00000017415
• Aliases: None
• Description: Sin3A-associated protein, 25kDa [Source:HGNC Symbol;Acc:41908]

Sequence

>retro_pabe_1129
GGGCAAGGACCAAGGGGCGAGCCCTGGAGCTCTGGAGCGGACGCCCCCAGGGAGCTGGGGTCACCCCCATGGGACAGCCC
TTCCTAGACCCGGAGAGAGCAGCTGCTGCTGCCCCACCACCCACCAGGCCCGGCCACTGAGCAGCGCCCCGGAGCCCCAG
ATCCTCGTTCCCCCCAGGTGGCCTGGGAGGTGGCCCCCTCGAGGATGACTCCACTAGCGCCCTGGGACCCCAAGTACGAA
GCCAAAGCAGGACCTTGGCTGGTGTGGGGGGCCAACTGTAGCTCAGGAGCCTCGTTCTGAGGCCGGACGCTGTGTCACCC
CTCGTTCTGGCCGCTGTACGAGGCAGCCTCGGGCAGGGGTCTCAGGCCCGTGGCCCCTGCCACAGGGCATTGTAATGGAC
AGCAGGCGCCCCCGGATGCAGGGTTCCCGGTGATGTGCTATGAAGACGTCTTCCTCTCGGATCCTCTGCTGCCCCGGGGG
CAGCGTGTCCCCCTATACCTGTCCAAGGCCCCCCAGCAGATGATGGGCTCCCTGAAACTGCTGCCGCCGCCCCCCATCAT
GTCTGCCAAGGTTCTCCCCCGCCTGTCACCCTCCCGGGGCCCCTCCACTGCCTGGCTCAGCGGGCCGGAGCTGATCGCTC
TCACTGGCCTGCTGCAGGTGAGCCAGGGGGAGCCTAGGCCCAGCTCCTCCGCAGCTGGCCCCCCAGACCCTACCTCTGAC
CCA

Alignment

ORF - retro_pabe_1129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.71 %
• Parental protein coverage: 50.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GEGAWGRCGCSLSPCPSS-PQPPSRSPSWTRREQLLLPHHPPGPATEQPPGAPDPRSPQVAWEVVPSRIT
          G.G..G....S....P.....PP..SPS.TRREQLLLPHHPPGPATEQ.PGAPDPRSPQVAWEV.PSR.T
Retrocopy GQGPRGEPWSSGADAPRELGSPPWDSPS*TRREQLLLPHHPPGPATEQRPGAPDPRSPQVAWEVAPSRMT

Parental  PLAPWDPKYEVKAGPRPVWGANCSSGASFSGRTLCHPSFWPLYEAASGRGLRPVAPATGHWNGQQAPPDA
          PLAPWDPKYE.KAGP..VWGANCSSGASF.GRTLCHPSFWPLYEAASGRGLRPVAPATGH.NGQQAPPDA
Retrocopy PLAPWDPKYEAKAGPWLVWGANCSSGASF*GRTLCHPSFWPLYEAASGRGLRPVAPATGHCNGQQAPPDA

Parental  GFPVMCCEDIFLSDPLLPRGQRVPLYLSKAPQQVRPSLQPSSPFPCSKPGLLHPPSPSKGPRFLAPLPFP
          GFPVMC.ED.FLSDPLLPRGQRVPLYLSKAPQQ...SL....P.P......L...SPS.GP.........
Retrocopy GFPVMCYEDVFLSDPLLPRGQRVPLYLSKAPQQMMGSLKLLPPPPIMSAKVLPRLSPSRGPSTAWLSGPE

Parental  LSRYPGLLRLSQTHPRPSTSPLPPPQESQMP
          L....GLL..SQ..PRPS.S...PP.....P
Retrocopy LIALTGLLQVSQGEPRPSSSAAGPPDPTSDP

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	0.06 RPM	2.32 RPM
SRP007412_cerebellum	0.00 RPM	2.68 RPM
SRP007412_heart	0.00 RPM	0.51 RPM
SRP007412_kidney	0.03 RPM	4.67 RPM
SRP007412_liver	0.03 RPM	2.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1129 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1129 has 0 orthologous retrocopies within eutheria group .

---

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,