RetrogeneDB ID: retro_ptro_1060

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:54651983..54652264(-)
• 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_1060
ATATATGAAGCCGAAATGCAGTGGAGGAGGGACTACAAAGTCGATCAAGAAATCGTCAGTATTATCCAGGAGCGGCTCAA
GACCTGTCAGTAGTGGGAAGAAGACAACCACAGGCAGAACTGGGCCAAGGAAGTGGAGCATTCACCCAGGTGGCCAAGGC
TTACCAGGACCGCTATCAGGACCTGGGGGCCCACCATTCTGCCAGGAAGTGCCGGGCCAAACAGAAGCAGAGGATGCTGG
AAGAGAGAAAAGCTGCAAAAGAGGCCACCGCTGCCGCCTCC

Alignment

ORF - retro_ptro_1060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.79 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYEAEMQWRRDYKVDQEIINIMQDRLKACQQREGQNYQQNCIKEVEQ-FTQVAKAYQDRYQDLGAYSSAR
          .YEAEMQWRRDYKVDQEI..I.Q.RLK.CQ..E..N..QN..KEVE..FTQVAKAYQDRYQDLGA..SAR
Retrocopy IYEAEMQWRRDYKVDQEIVSIIQERLKTCQ*WEEDNHRQNWAKEVEH<FTQVAKAYQDRYQDLGAHHSAR

Parental  KCLAKQRQRMLQERKAAKEAAAATS
          KC.AKQ.QRML.ERKAAKEA.AA.S
Retrocopy KCRAKQKQRMLEERKAAKEATAAAS

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	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_1060 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1060 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1573
Gorilla gorilla	retro_ggor_1198
Pongo abelii	retro_pabe_1297
Macaca mulatta	retro_mmul_2218

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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,