RetrogeneDB ID: retro_mmul_2498

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:62304962..62306104(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009813
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.681
• Ensembl ID: ENSMMUG00000002194
• Aliases: None
• Description: None

Sequence

>retro_mmul_2498
ATGGAGTCTGGCAGTACTGCCGCCAGCGAGGAGGCACGCAGCCTTCAAGAATGTGAACTCTACGTCCAGAAGCATAACAT
TCAAGCACTGCTCAAAGATTCTATTGTGCAGTTGTGCACTGCTCGACCTGAGAGACTCATGGTATTCCTCAGGGAATACT
TTGAGAGGTTGGAGAAGGAGGAGACAAAACAGATTCAGAATCTGCAGAAAGCAGGCACTCGTACAGACTCAAGGGAAGAT
GAGATCTCTCCTCCTCCACCCAACCCAGTGGTTAAAGGTCGGAGGCGACGAGGGCTATTAGCGCTGAGGTCTACACGGAG
GAAGATGCCACATCATATGTTAGAAAGGTTATACCAAAAGATTACAAGACGATGGCTGCTTTAGCCAAAGCCATTGAGAA
GAATGTGCTGTTTTCACATCTTGATGATAATGAGAGAAGTGATATTTTTGATGCCATGTTTTCGGTCTCCTTTATCGCAG
GAGAGACTGTGATTCAGCAAGGTGATAAAGGGGATAACTTCTATGTGATTGATCAAGGAGAGACGGATGTCTATGTCAAC
AATGAATGGGCAACTAGTGTTGGGGAAGGAGGGAGCTTTGGAGAACTTGCTTTGATTTATGGAACACCTAGAGCAGCCAC
TGTCAAAGCAAAGACAAATGTGAAATTGTGGGGCATCGACCAAGACAGCTATAGAAGAATCCTCATGGGAAGCACACTGA
GAAAGCGGAAGATGTATGAGGAACTCCTCAGTAAAGTCTCTATTCTAGAGTCTCTGGACAAGTGGGAACGTCTTACCGTA
GCTGATGCATTGGAACCAGTGCAGTTTGAAGATGGGCAGAAGATTGTGGTGCAGGGAGAACCAGGGGATGAGTTCTTCAT
TATTTTAGAGGGGTCAGCTGCTGTGCTACAACGTCACTCAGAAAATGAAGAGTTTGTTGAAGTGGGAAGATTGGGGCCTT
CTGATTATTTTGGTGAAATTGCACTACTGATGAATCGTCCTCGTGCTGCCACAGTCGTTGCTCGTGGCCCCTTGAAGTGC
GTTAAGCTGGACCGACCTAGATTTGAATGTGTTCTTGGCCCATGCTCAGACATCCTCAAACGAAACATCCAGCAGTACAA
CAGTTTTGTGTCACTGTCTGTC

Alignment

ORF - retro_mmul_2498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MESGSTAASEEARSLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFERLEKEEAKQIQNLQK
          MESGSTAASEEARSL.ECELYVQKHNIQALLKDSIVQLCTARPER.M.FLREYFERLEKEE.KQIQNLQK
Retrocopy MESGSTAASEEARSLQECELYVQKHNIQALLKDSIVQLCTARPERLMVFLREYFERLEKEETKQIQNLQK

Parental  AGTRTDSREDEISPPPPNPVVKGRRRRG-AISAEVYTEEDATSYVRKVIPKDYKTMAALAKAIEKNVLFS
          AGTRTDSREDEISPPPPNPVVKGRRRRG.AISAEVYTEEDATSYVRKVIPKDYKTMAALAKAIEKNVLFS
Retrocopy AGTRTDSREDEISPPPPNPVVKGRRRRG<AISAEVYTEEDATSYVRKVIPKDYKTMAALAKAIEKNVLFS

Parental  HLDDNERSDIFDAMFSVSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVGEGGSFGELALIYGT
          HLDDNERSDIFDAMFSVSFIAGETVIQQGD.GDNFYVIDQGETDVYVNNEWATSVGEGGSFGELALIYGT
Retrocopy HLDDNERSDIFDAMFSVSFIAGETVIQQGDKGDNFYVIDQGETDVYVNNEWATSVGEGGSFGELALIYGT

Parental  PRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDG
          PRAATVKAKTNVKLWGID.DSYRRILMGSTLRKRKMYEE.LSKVSILESLDKWERLTVADALEPVQFEDG
Retrocopy PRAATVKAKTNVKLWGIDQDSYRRILMGSTLRKRKMYEELLSKVSILESLDKWERLTVADALEPVQFEDG

Parental  QKIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVK
          QKIVVQGEPGDEFFIILEGSAAVLQR.SENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVK
Retrocopy QKIVVQGEPGDEFFIILEGSAAVLQRHSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVK

Parental  LDRPRFERVLGPCSDILKRNIQQYNSFVSLSV
          LDRPRFE.VLGPCSDILKRNIQQYNSFVSLSV
Retrocopy LDRPRFECVLGPCSDILKRNIQQYNSFVSLSV

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	0.45 RPM	388.70 RPM
SRP007412_brain_prefrontal_cortex	2.30 RPM	338.34 RPM
SRP007412_cerebellum	0.19 RPM	316.29 RPM
SRP007412_heart	0.82 RPM	353.02 RPM
SRP007412_kidney	0.00 RPM	229.81 RPM
SRP007412_liver	0.04 RPM	76.91 RPM
SRP007412_testis	0.64 RPM	235.40 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2498 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108946	1 retrocopy	retro_hsap_186,
Gorilla gorilla	ENSGGOG00000016507	1 retrocopy	retro_ggor_267,
Macaca mulatta	ENSMMUG00000002194	2 retrocopies	retro_mmul_2498 , retro_mmul_393,
Nomascus leucogenys	ENSNLEG00000001982	1 retrocopy	retro_nleu_996,
Pan troglodytes	ENSPTRG00000009579	1 retrocopy	retro_ptro_172,
Ictidomys tridecemlineatus	ENSSTOG00000012903	1 retrocopy	retro_itri_104,