RetrogeneDB ID: retro_mmul_538

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:147311853..147312091(-)
• Located in intron of: ENSMMUG00000005873

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB1
• Ensembl ID: ENSMMUG00000022428
• Aliases: None
• Description: None

Sequence

>retro_mmul_538
GTGGCTGAGCTTGTCACTACCCTTGGTTGTGGAGTCATTGTTGGAACCGGGGCTTTTGCAATCATGGTGGACTGACTTCA
GACTGTGTATGACCACTGGGTCCACAGACTTGTCCGTATAGGATTTGTCTTTGTGTGTTATCTAAAGAGAAAGAATGATG
GAAAAGCTAACTGCCTTCTGGAAAAAAAAGTATGTTATTTAAAAGGGAATTGAGACCCATGGAGAAGTTGCTTGGAAG

Alignment

ORF - retro_mmul_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.2 %
• Parental protein coverage: 76.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LARVAVALGLGVPVGTEAAAIMVNLLQIVRDHWVHVLVPMGFVIGCYLDRKND-ERLTAF-RNKSALFKR
          .A.....LG.GV.VGT.A.AIMV..LQ.V.DHWVH.LV..GFV..CYL.RKND.E.LTAF......LFKR
Retrocopy VAELVTTLGCGVIVGTGAFAIMVD*LQTVYDHWVHRLVRIGFVFVCYLKRKND>EKLTAF>XXXXMLFKR

Parental  ELRPNE-EVTWK
          ELRP.E.EV.WK
Retrocopy ELRPME<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	0.00 RPM	41.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	39.43 RPM
SRP007412_cerebellum	0.00 RPM	46.04 RPM
SRP007412_heart	0.00 RPM	97.04 RPM
SRP007412_kidney	0.23 RPM	70.19 RPM
SRP007412_liver	0.00 RPM	47.70 RPM
SRP007412_testis	0.00 RPM	18.85 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_538 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_538 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_311
Pan troglodytes	retro_ptro_253

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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,