RetrogeneDB ID: retro_mmul_951

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:54726734..54727199(-)
• Located in intron of: ENSMMUG00000005613

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1094
• Ensembl ID: ENSMMUG00000021721
• Aliases: None
• Description: RAB1A, member RAS oncogene family [Source:RefSeq peptide;Acc:NP_001244201]

Sequence

>retro_mmul_951
AATCCCAAATATGATTATTTATTCAAATTACTTCTGATTGGCGACTCTGGGGCTGGAAGGTCTTGCCTCCTTCTTAGGTT
TGCAGATGATACATATACAGAAAGCTACATCAGCACAGTTGGTGGGGATTTCAAAATAAGAACTATAGAGTTAGATGGGA
AAACAATCAAGCTTCAAATATGGAACACGGCAGAACAGGAAAGATTTCGAACAGTCATCTCCAGTTGTTACAGAGGAGCC
AGGGGCATCCTGGTTGTGTATGATGTGACAGATCAGGAGTCCTTGAATAATATTAAACAGTGACTGCAGAAAATAGATCA
TTATCCCAGTGAAAACATCAACAGATTGTTGGTAGGGAACAAGTGTGATCTGACCACAAAGAAAGTAGTAGACTACACAA
CAGCAAAGGAATTTGCTGATTCCCTTGGAATTCTGTTTTTGGAAACCAGTGCTAAGAATGCAACA

Alignment

ORF - retro_mmul_951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.16 %
• Parental protein coverage: 75.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NNENDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFR
          N...DYLFKLLLIGDSG.G.SCLLLRFADDTYTESYIST.G.DFKIRTIELDGKTIKLQIW.TA.QERFR
Retrocopy NPKYDYLFKLLLIGDSGAGRSCLLLRFADDTYTESYISTVGGDFKIRTIELDGKTIKLQIWNTAEQERFR

Parental  TITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFAD
          T..SS.YRGA.GI.VVYDVTDQES.NN.KQ.LQ.ID.Y.SEN.N.LLVGNKCDLTTKKVVDYTTAKEFAD
Retrocopy TVISSCYRGARGILVVYDVTDQESLNNIKQ*LQKIDHYPSENINRLLVGNKCDLTTKKVVDYTTAKEFAD

Parental  SLGIPFLETSAKNAT
          SLGI.FLETSAKNAT
Retrocopy SLGILFLETSAKNAT

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	19.72 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	47.36 RPM
SRP007412_cerebellum	0.13 RPM	12.27 RPM
SRP007412_heart	0.06 RPM	9.83 RPM
SRP007412_kidney	0.00 RPM	21.24 RPM
SRP007412_liver	0.04 RPM	8.59 RPM
SRP007412_testis	0.00 RPM	17.34 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_951 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_951 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_951 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000002112	1 retrocopy	retro_dord_305,
Echinops telfairi	ENSETEG00000002205	2 retrocopies	retro_etel_1687, retro_etel_413,
Homo sapiens	ENSG00000138069	2 retrocopies	retro_hsap_2362, retro_hsap_3626,
Macaca mulatta	ENSMMUG00000017586	1 retrocopy	retro_mmul_324,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951 ,
Oryctolagus cuniculus	ENSOCUG00000017003	1 retrocopy	retro_ocun_800,
Pongo abelii	ENSPPYG00000012360	1 retrocopy	retro_pabe_2135,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Ictidomys tridecemlineatus	ENSSTOG00000020693	1 retrocopy	retro_itri_1541,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,