RetrogeneDB ID: retro_pabe_3106

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:138588535..138588840(+)
• Located in intron of: ENSPPYG00000029654

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB10
• Ensembl ID: ENSPPYG00000006974
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001124813]

Sequence

>retro_pabe_3106
ATGCCAGAGAGCTGGGACAAGGATGTGTACCCTAAGTCCCCATGCCCTCGCTCCAGGCCTTGCTCCACAAACCCATCACC
TACTTGATGAAGGCCTTTGACCTCCTCATGGCCTTTGTGAGAGAGAGTTTATAAAGGGGCAGCATGTGAAGAAGGTATTA
TTACTACCAGTGGGAGTATTGCCGCATGCCAGACATCATTGAGTGCAAGGAGGATGTTTTGTGCATGTTTGGAGCTGAAA
TGCAATGGAGAAGGGACCACAAAGTCAATGAAGAAATTGCTGGCATCATCCAGGAGAGGCTTAAG

Alignment

ORF - retro_pabe_3106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 61.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPDSWDKDVYPEPP--RRTP-VLPNPIVYMMKAFDLIVDRPVTLAREFVERQHAKNRYYYYHRQYRRVPD
          MP.SWDKDVYP..P..R..P..L..PI.Y.MKAFDL.........RE...R.....RYYYY...Y.R.PD
Retrocopy MPESWDKDVYPKSPCPRSRP<LLHKPITYLMKAFDLLM----AFVRESL*RGSM*RRYYYYQWEYCRMPD

Parental  ITECKEEDIMCMYEAEMQWRRDYKVDQEIINIMQDRLK
          I.ECKE.D..CM..AEMQWRRD.KV..EI..I.Q.RLK
Retrocopy IIECKE-DVLCMFGAEMQWRRDHKVNEEIAGIIQERLK

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	43.73 RPM
SRP007412_cerebellum	0.00 RPM	38.79 RPM
SRP007412_heart	0.15 RPM	91.18 RPM
SRP007412_kidney	0.00 RPM	73.12 RPM
SRP007412_liver	0.00 RPM	32.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3106 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3106 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3801
Pan troglodytes	retro_ptro_2578
Gorilla gorilla	retro_ggor_2555

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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,