RetrogeneDB ID: retro_mmul_870

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:56204468..56205204(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1739
• Ensembl ID: ENSMMUG00000013616
• Aliases: None
• Description: methyltransferase like 15 [Source:RefSeq peptide;Acc:NP_001247884]

Sequence

>retro_mmul_870
ATGCTTTGGTATCCATATTTTTGTAGAATGTATAAAGAATGTCTTTCATGTTGGTTGGAATCTGGCATACCTAGGTTAGG
TGTCTAGACAAAAAAGAATATATACTACAGCAGAAAAATGTAAAGAATATGAAGCCTAGAAGCAAAAAGATCAAACTCAA
GCCCAGGAGTTACACAGATCTCAAGATAGAGATTTTGAAACTATGGCTAAATTACATATTCCAGTAATGGTGGATGAAGT
TGTTCATTGGTCGTCACCACAAAAAAGACAGATTTTTCTAGATATGACATTTGGTTAGGGAGGGCGCGCAAAAGCCATTC
TACAGAAGGAGTCAGATATTGTTCTGTGGGCCTTGGACAGAGACCCGACAGCTTATGCATTCACTGAACATCTTTCAGAG
TTGTATCGTAAACAAATCTGAGCTATGCTGGGCCAGTTCAGCCAGGCAGAAGCCTTGTTAATGAAAGCTGGAGTGCAGCC
AGGGACTTTCGATGGAGTTCGTATGGATCTTGGGTGTTCTTACGTGTAACTCAATACTCCTGAAAGAGATTTTTCCCTTC
GGAAAGGTGGCCCCTTGGACATGAGGATGGATGGTAGCAGGTACCCTGACACTCCCACTGCTGCTGATGTTTTCAATGCT
TTAGATCAACAGGCACTTGCATGTATCCTGAGAACATACGAGGAGGAAAAGCATGCCAAGAAAATTGCTTCACCAATTGT
TCAGGCACGCAGCATC

Alignment

ORF - retro_mmul_870 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.74 %
• Parental protein coverage: 94.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRYPYFCRMYKECLSCWLASGIPNLGV-WPKRIHTTAEKYGEYEAQEQTDQTQAQELHRSQDRDFETMA
          ML.YPYFCRMYKECLSCWL.SGIP.LGV...KRI.TTAEK..EYEA..Q.DQTQAQELHRSQDRDFETMA
Retrocopy MLWYPYFCRMYKECLSCWLESGIPRLGV>RQKRIYTTAEKCKEYEA*KQKDQTQAQELHRSQDRDFETMA

Parental  KLHIPVMVDEVVHCLSPQKGQIFLDMTFGSGGHTKAILQKESDIVLYALDRDPTAYALAEHLSELYPKQI
          KLHIPVMVDEVVH..SPQK.QIFLDMTFG.GG..KAILQKESDIVL.ALDRDPTAYA..EHLSELY.KQI
Retrocopy KLHIPVMVDEVVHWSSPQKRQIFLDMTFG*GGRAKAILQKESDIVLWALDRDPTAYAFTEHLSELYRKQI

Parental  RAVLGQFSQAEALLTKAGVQPGTFDGVLMDLGCSSMQLDTPERGFSLRKDGPLDMRMDGGRYPDMPTAAD
          .A.LGQFSQAEALL.KAGVQPGTFDGV.MDLGCS...L.TPER.FSLRK.GPLDMRMDG.RYPD.PTAAD
Retrocopy *AMLGQFSQAEALLMKAGVQPGTFDGVRMDLGCSYV*LNTPERDFSLRKGGPLDMRMDGSRYPDTPTAAD

Parental  VVNALDQPALASILRTYGEEKHARKIASAIVQARSI
          V.NALDQ.ALA.ILRTY.EEKHA.KIAS.IVQARSI
Retrocopy VFNALDQQALACILRTYEEEKHAKKIASPIVQARSI

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	5.60 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.79 RPM
SRP007412_cerebellum	0.00 RPM	4.46 RPM
SRP007412_heart	0.00 RPM	6.01 RPM
SRP007412_kidney	0.00 RPM	8.33 RPM
SRP007412_liver	0.00 RPM	4.75 RPM
SRP007412_testis	0.00 RPM	11.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_870 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_870 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_870 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1123
Pan troglodytes	retro_ptro_680
Callithrix jacchus	retro_cjac_3301

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006142	2 retrocopies	retro_cjac_3301, retro_cjac_4047,
Homo sapiens	ENSG00000169519	2 retrocopies	retro_hsap_1123, retro_hsap_4656,
Macaca mulatta	ENSMMUG00000013616	1 retrocopy	retro_mmul_870 ,
Nomascus leucogenys	ENSNLEG00000017865	2 retrocopies	retro_nleu_1093, retro_nleu_187,
Oryctolagus cuniculus	ENSOCUG00000014291	1 retrocopy	retro_ocun_536,
Pongo abelii	ENSPPYG00000003399	1 retrocopy	retro_pabe_3617,
Pan troglodytes	ENSPTRG00000003461	1 retrocopy	retro_ptro_680,