RetrogeneDB ID: retro_ptro_2578

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:142817383..142817686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB10
• Ensembl ID: ENSPTRG00000007618
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa (NDUFB10), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071824]

Sequence

>retro_ptro_2578
ATGCCAGAGAGCTGGGACAAGGATGTGTACCCCAAGTCCCCATGCCCTCGCTGCAGGCCTTGCTCCCCAAACCCATCACC
TACTTGATGAAGGCCTTTGACCTCCTCATGGCCTTTGTGAGAGAGTTTATAAAGGGGCAGCATGTGAAGAAGGTATTACT
ACTACCACTGGGAGTATCGCCACATGCCAGACATCATTGAATGCAAGGAGGATGTTTTGTGCATGTTTGGAGCTGAAATG
CAATGGAGAAGGGACCACAAAATCAGTCAAGAAATTGTTGACCTCATCCAGGAGAGGCTTAAG

Alignment

ORF - retro_ptro_2578 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.8 %
• Parental protein coverage: 61.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPDSWDKDVYPEP--PRRTPVQPN-LIVYMMKAFDLIVDRPVTLVREFIERQHAK-NRYYYYHRQYRRVP
          MP.SWDKDVYP....PR..P..PN..I.Y.MKAFDL........VREFI..QH.K...YY.YH..YR..P
Retrocopy MPESWDKDVYPKSPCPRCRPCSPN<PITYLMKAFDLL----MAFVREFIKGQHVK>RYYY-YHWEYRHMP

Parental  DITECKEEDIMCMYEAEMQWRRDYKVDQEIINIMQDRLK
          DI.ECK.ED..CM..AEMQWRRD.K..QEI....Q.RLK
Retrocopy DIIECK-EDVLCMFGAEMQWRRDHKISQEIVDLIQERLK

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	54.87 RPM
SRP007412_cerebellum	0.00 RPM	37.39 RPM
SRP007412_heart	0.00 RPM	111.19 RPM
SRP007412_kidney	0.00 RPM	91.98 RPM
SRP007412_liver	0.00 RPM	49.13 RPM
SRP007412_testis	0.00 RPM	38.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2578 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2578 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2578 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3801
Gorilla gorilla	retro_ggor_2555
Pongo abelii	retro_pabe_3106

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019476	1 retrocopy	retro_cfam_1861,
Echinops telfairi	ENSETEG00000017154	1 retrocopy	retro_etel_1955,
Felis catus	ENSFCAG00000011738	1 retrocopy	retro_fcat_307,
Homo sapiens	ENSG00000140990	2 retrocopies	retro_hsap_1573, retro_hsap_3801,
Gorilla gorilla	ENSGGOG00000009367	2 retrocopies	retro_ggor_1198, retro_ggor_2555,
Latimeria chalumnae	ENSLACG00000013152	1 retrocopy	retro_lcha_100,
Macaca mulatta	ENSMMUG00000029268	1 retrocopy	retro_mmul_2218,
Mus musculus	ENSMUSG00000040048	1 retrocopy	retro_mmus_2566,
Nomascus leucogenys	ENSNLEG00000008867	1 retrocopy	retro_nleu_1740,
Pongo abelii	ENSPPYG00000006974	2 retrocopies	retro_pabe_1297, retro_pabe_3106,
Pan troglodytes	ENSPTRG00000007618	2 retrocopies	retro_ptro_1060, retro_ptro_2578 ,
Rattus norvegicus	ENSRNOG00000014568	1 retrocopy	retro_rnor_1056,
Sus scrofa	ENSSSCG00000030328	1 retrocopy	retro_sscr_689,