RetrogeneDB ID: retro_mmul_2280

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:18896844..18897187(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18828
• Ensembl ID: ENSMMUG00000022419
• Aliases: C8H8orf46, C8orf46
• Description: chromosome 8 open reading frame 46 [Source:RefSeq peptide;Acc:NP_001181830]

Sequence

>retro_mmul_2280
GTGGAGATTTCTGAACCCAAAGCATCAAATCTGTATAGGAAGAATCGAGCACATGGAAAAATCTTTGACTGCTCCAGTGT
CTCGGATCTCAATGAAAGCTCCAGCCTCAGCCTTGGTGGAGGCAGCAGCCCTGGGCTCAGAGAAGGAAGGTATTCAGATG
ACAGGATTCAGACCTCTCAGGATGACCAAAGAGTATCTAAGCATTCACCAAGGAGCAGAAGCCTCCCTATCGCTGACAGG
CAGTACTTCCTGCGGTGTCCCCAGCAGCCCCCGGAAACTGTGGACAAGGCACAAGAAGACGCCTGAATATGTGAGAGCCA
CCGACACTGCCTTTCAGGCCGAC

Alignment

ORF - retro_mmul_2280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.34 %
• Parental protein coverage: 55.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGISEPKTSNLCG-NRAYGK-SLIPPVPRISVKTPTSASLEATVMGTEKGAVLMRGSRHLKKMTEEYPAL
          V.ISEPK.SNL...NRA.GK.SL..PV.RIS.K.P.SA..EA...G.EK....M.G.R.L..MT.EY...
Retrocopy VEISEPKASNLYRKNRAHGK>SLTAPVSRISMKAPASALVEAAALGSEKEGIQMTGFRPLR-MTKEYLSI

Parental  PQGVEASLPLTGSASCGVPGILRKMWTRHKKKSEYVGATNSAFEAD
          .QG.EASL.LTGS.SCGVP...RK.WTRHKK..EYV.AT..AF.AD
Retrocopy HQGAEASLSLTGSTSCGVPSSPRKLWTRHKKTPEYVRATDTAFQAD

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	157.54 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	185.47 RPM
SRP007412_cerebellum	0.00 RPM	9.75 RPM
SRP007412_heart	0.06 RPM	10.30 RPM
SRP007412_kidney	0.00 RPM	0.35 RPM
SRP007412_liver	0.12 RPM	0.20 RPM
SRP007412_testis	0.04 RPM	0.23 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2280 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2280 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3937
Pan troglodytes	retro_ptro_2673
Gorilla gorilla	retro_ggor_2646

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169085	1 retrocopy	retro_hsap_3937,
Gorilla gorilla	ENSGGOG00000008516	1 retrocopy	retro_ggor_2646,
Macaca mulatta	ENSMMUG00000022419	1 retrocopy	retro_mmul_2280 ,
Nomascus leucogenys	ENSNLEG00000010728	1 retrocopy	retro_nleu_634,
Pongo abelii	ENSPPYG00000018639	2 retrocopies	retro_pabe_3245, retro_pabe_3378,
Pan troglodytes	ENSPTRG00000020307	1 retrocopy	retro_ptro_2673,
Tupaia belangeri	ENSTBEG00000014906	1 retrocopy	retro_tbel_1795,