RetrogeneDB ID: retro_mmul_1182

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:45906479..45907015(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3888
• Ensembl ID: ENSMMUG00000006899
• Aliases: None
• Description: None

Sequence

>retro_mmul_1182
GGCAACCTGGCCTCTGGCAGCGTGGCAGTCGTGTATCCCCTGGATTTCACCAGAATCTGCCTGGCAGCCGACGTGGAAAA
GTCGGGCACGGAGAGCGAGTTCCGAGGCCTGGGAGACTGCCTGGTGAAGATCCCCAAGTCCGACGGCATCCGGGGCCTGT
ACCAGGGCTTCAGCGTCTCCGTGCAGGGCATCATCATCTACCAGGCCGCCTGCTTGGGGTGTACGATACGGCCAAGGGCA
TGCTCCCCGACCTCAAGAACACGCACATCCTGGTGAGCTGGATGATCGCGCAGACCGTGACTGCCATGGCTGGCGTGGTG
TCCTACCCCTTCGACACAGTGCGGCGGCAGATGATGACGCAGTCCGGGCGCAAAGGAGCTGACGTCATGTACACGGGCAC
CGCAGACTGTTGGAGGAAGATCTTCAGAGACGAGGCGGCCAAGGCCTTTTTCAAGGGTGCGTGGTCCAACGTCCTCAGAG
GCATGGGGGTGGGGGCGGGTTTCGTGCTGGTCCTGTATGACGAGCTGAAGAAGGTA

Alignment

ORF - retro_mmul_1182 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 67.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAAGATSLCFVYPLDFARTRLAADVGKSGTEREFRGLGDCLVKITKSDGIRGLYQGFSVSVQGIIIYRAA
          G.....S...VYPLDF.R..LAADV.KSGTE.EFRGLGDCLVKI.KSDGIRGLYQGFSVSVQGIIIY.AA
Retrocopy GNLASGSVAVVYPLDFTRICLAADVEKSGTESEFRGLGDCLVKIPKSDGIRGLYQGFSVSVQGIIIYQAA

Parental  -YFGVYDTAKGMLPDPKNTHIVVSWMIAQTVTAVAGVVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWR
          ...GVYDTAKGMLPD.KNTHI.VSWMIAQTVTA.AGVVSYPFDTVRR.MM.QSGRKGAD.MYTGT.DCWR
Retrocopy <LLGVYDTAKGMLPDLKNTHILVSWMIAQTVTAMAGVVSYPFDTVRRQMMTQSGRKGADVMYTGTADCWR

Parental  KIFRDEGGKAFFKGAWSNVLRGMG--GAFVLVLYDELKKV
          KIFRDE..KAFFKGAWSNVLRGMG....FVLVLYDELKKV
Retrocopy KIFRDEAAKAFFKGAWSNVLRGMGVGAGFVLVLYDELKKV

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	123.48 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	458.61 RPM
SRP007412_cerebellum	0.00 RPM	122.89 RPM
SRP007412_heart	0.06 RPM	82.20 RPM
SRP007412_kidney	0.00 RPM	205.63 RPM
SRP007412_liver	0.00 RPM	138.86 RPM
SRP007412_testis	0.94 RPM	23.97 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1182 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1182 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4147

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005609	1 retrocopy	retro_amel_255,
Homo sapiens	ENSG00000169100	5 retrocopies	retro_hsap_1207, retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla	ENSGGOG00000023004	2 retrocopies	retro_ggor_239, retro_ggor_2785,
Loxodonta africana	ENSLAFG00000001584	1 retrocopy	retro_lafr_713,
Microcebus murinus	ENSMICG00000006136	2 retrocopies	retro_mmur_1021, retro_mmur_922,
Macaca mulatta	ENSMMUG00000006899	1 retrocopy	retro_mmul_1182 ,
Macaca mulatta	ENSMMUG00000022663	6 retrocopies	retro_mmul_1022, retro_mmul_1287, retro_mmul_1699, retro_mmul_1775, retro_mmul_1800, retro_mmul_2090,
Nomascus leucogenys	ENSNLEG00000000389	1 retrocopy	retro_nleu_895,
Otolemur garnettii	ENSOGAG00000000963	2 retrocopies	retro_ogar_2492, retro_ogar_2499,