RetrogeneDB ID: retro_ptro_253

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:202215465..202215695(+)
• Located in intron of: ENSPTRG00000002013

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB1
• Ensembl ID: ENSPTRG00000006649
• Aliases: None
• Description: Pan troglodytes NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa (NDUFB1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001076782]

Sequence

>retro_ptro_253
GAGCTCGTCACTACCCTTGGTTGTGGGGTCATTGTTGGAACCGGGGCTTTTGCAGTCATGGTGGACTGACTTGAGACTGT
GTATGAGCACTGGGTCCATAGACTTGTCCGTATAGGATTTGTCTTTGTATGTTGTCTAAAGAGAAAGAATGATGAAAAGC
TAACTGCCTTCTGGAAAAATAGTATTTTATTTAAAAGGGAATTGAGACCCATGGAGAAGTTGCTTGGAAG

Alignment

ORF - retro_ptro_253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.69 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EFPVALGLGVAVGAEAAAIMVNLLQIVRDHWVHVLVPMGFVIGCYLDRKSDERLTAFRNKSMLFKRELQP
          E....LG.GV.VG..A.A.MV..L..V..HWVH.LV..GFV..C.L.RK.DE.LTAF...S.LFKREL.P
Retrocopy ELVTTLGCGVIVGTGAFAVMVD*LETVYEHWVHRLVRIGFVFVCCLKRKNDEKLTAFWKNSILFKRELRP

Parental  SE-EVTWK
          .E.EV.WK
Retrocopy ME<EVAWK

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	35.30 RPM
SRP007412_cerebellum	0.00 RPM	18.53 RPM
SRP007412_heart	0.06 RPM	80.85 RPM
SRP007412_kidney	0.05 RPM	56.72 RPM
SRP007412_liver	0.00 RPM	32.64 RPM
SRP007412_testis	0.11 RPM	10.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_253 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_253 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_311
Macaca mulatta	retro_mmul_538

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014837	1 retrocopy	retro_amel_1060,
Callithrix jacchus	ENSCJAG00000018067	5 retrocopies	retro_cjac_1027, retro_cjac_1053, retro_cjac_1330, retro_cjac_2586, retro_cjac_3294,
Homo sapiens	ENSG00000183648	2 retrocopies	retro_hsap_2646, retro_hsap_311,
Macaca mulatta	ENSMMUG00000022428	2 retrocopies	retro_mmul_1520, retro_mmul_538,
Nomascus leucogenys	ENSNLEG00000017129	1 retrocopy	retro_nleu_652,
Ochotona princeps	ENSOPRG00000012731	2 retrocopies	retro_opri_22, retro_opri_992,
Pongo abelii	ENSPPYG00000006076	1 retrocopy	retro_pabe_2325,
Pan troglodytes	ENSPTRG00000006649	2 retrocopies	retro_ptro_1782, retro_ptro_253 ,
Pteropus vampyrus	ENSPVAG00000015319	1 retrocopy	retro_pvam_642,
Tursiops truncatus	ENSTTRG00000008130	2 retrocopies	retro_ttru_1515, retro_ttru_830,
Vicugna pacos	ENSVPAG00000003502	2 retrocopies	retro_vpac_257, retro_vpac_39,