RetrogeneDB ID: retro_ptro_2656

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:133246981..133247446(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB9
• Ensembl ID: ENSPTRG00000020569
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa (NDUFB9), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071799]

Sequence

>retro_ptro_2656
GTGGCGTTCTCCGCACCGGCTGCCTACCTGACCCATCAGCAGAAGGTGTTGAGGCTTTAAAAGTGGGTGCTGTGCCACCT
CGAGTTGTGTTGCATCCACAGGGACAAATACCGATACTTTGCTTGTTTGATGAGAGCCCGGTCTGAAGAACATACGAACG
AAAAGGATATGATGAAGGCCACCCGGCTGCTGAAGGAGGCTGAGGAAGAATTCTGGTACCATCAGCATCCACAGCCATAC
ATCTTCCCTGACTCTCCTAGGGGTACCTCCTATGTGACACACGAGTGCTACAAGGTCCCAGAATGGTGCTTAGATGACTG
GCATCCTTCTGAGAAGGCAATGTATCCTGATTACTTTGCCAAGAGAAAACAGTGGAAGAAACTGCGGAGGGAAAGCTGGA
AAAGAGAGGTTAAGCAGCTGCAGGAGGAAACGCCACCTGCCGGAAAGGAAGGTGATTTGCCCCCA

Alignment

ORF - retro_ptro_2656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 87.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFLASGPYLTHQQKVLRLYKRALRHLESWCVQRDKYRYFACLMRARFEEHKNEKDMAKATQLLKEAEEE
          .AF.A...YLTHQQKVLRL.K..L.HLE..C..RDKYRYFACLMRAR.EEH.NEKDM.KAT.LLKEAEEE
Retrocopy VAFSAPAAYLTHQQKVLRL*KWVLCHLELCCIHRDKYRYFACLMRARSEEHTNEKDMMKATRLLKEAEEE

Parental  FWYRQHPQPYIFPDSPGGTSYERYDCYKVPEWCLDDWHPSEKAMYPDYFAKREKWKKLRRESWEREVKQL
          FWY.QHPQPYIFPDSP.GTSY....CYKVPEWCLDDWHPSEKAMYPDYFAKR..WKKLRRESW.REVKQL
Retrocopy FWYHQHPQPYIFPDSPRGTSYVTHECYKVPEWCLDDWHPSEKAMYPDYFAKRKQWKKLRRESWKREVKQL

Parental  QEETPPGGPLTEALPP
          QEETPP.G.....LPP
Retrocopy QEETPPAGKEGD-LPP

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	128.73 RPM
SRP007412_cerebellum	0.00 RPM	72.45 RPM
SRP007412_heart	0.09 RPM	132.47 RPM
SRP007412_kidney	0.05 RPM	140.28 RPM
SRP007412_liver	0.03 RPM	97.45 RPM
SRP007412_testis	0.00 RPM	67.97 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2656 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2656 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3905
Gorilla gorilla	retro_ggor_2632
Pongo abelii	retro_pabe_3182

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010022	1 retrocopy	retro_acar_132,
Ailuropoda melanoleuca	ENSAMEG00000015852	2 retrocopies	retro_amel_1680, retro_amel_553,
Callithrix jacchus	ENSCJAG00000012818	1 retrocopy	retro_cjac_2125,
Equus caballus	ENSECAG00000018238	1 retrocopy	retro_ecab_541,
Felis catus	ENSFCAG00000004678	1 retrocopy	retro_fcat_689,
Homo sapiens	ENSG00000147684	2 retrocopies	retro_hsap_3905, retro_hsap_4112,
Gorilla gorilla	ENSGGOG00000015883	2 retrocopies	retro_ggor_2632, retro_ggor_2759,
Microcebus murinus	ENSMICG00000017481	1 retrocopy	retro_mmur_1494,
Myotis lucifugus	ENSMLUG00000003765	1 retrocopy	retro_mluc_1339,
Macaca mulatta	ENSMMUG00000015493	1 retrocopy	retro_mmul_1736,
Monodelphis domestica	ENSMODG00000001831	3 retrocopies	retro_mdom_1176, retro_mdom_1193, retro_mdom_1582,
Nomascus leucogenys	ENSNLEG00000005484	2 retrocopies	retro_nleu_1141, retro_nleu_578,
Otolemur garnettii	ENSOGAG00000030772	2 retrocopies	retro_ogar_1654, retro_ogar_925,
Pongo abelii	ENSPPYG00000018869	3 retrocopies	retro_pabe_2643, retro_pabe_3182, retro_pabe_3366,
Pan troglodytes	ENSPTRG00000020569	2 retrocopies	retro_ptro_2656 , retro_ptro_2791,
Pteropus vampyrus	ENSPVAG00000009153	1 retrocopy	retro_pvam_243,
Ictidomys tridecemlineatus	ENSSTOG00000021955	1 retrocopy	retro_itri_611,
Tupaia belangeri	ENSTBEG00000006895	3 retrocopies	retro_tbel_1901, retro_tbel_2663, retro_tbel_610,