RetrogeneDB ID: retro_mmul_359

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:24071072..24071448(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R11
• Ensembl ID: ENSMMUG00000012122
• Aliases: None
• Description: Protein phosphatase 1 regulatory subunit 11 [Source:UniProtKB/Swiss-Prot;Acc:Q5TM51]

Sequence

>retro_mmul_359
ATGGCCGAGGCAGGGGCTGGGCTGAGCGAGACTGTCACTGAGACAACGGTTACCGTGACAACCGAGCCCGAGAACCGCAG
CTTTACCATCAAACTTCGGAAACGGAAACCAGAGAAAAAGGTGGAATGGACAAGTGACACTGTGGACAATGAGCGCATGC
GCCGCCGCTCATCAAAATGCTGTTGTATTTATGAAAAACCCCGGGGCTTTTGGCGACAGCTCCACGGAAAGTGATGAGGA
GGAAGAAGAGGGCTGTGGTCATACACACTGTGTACGTGGCCACCGCAAAGGATGGCGTCGTGCAACCCTGGGACCGACCC
CCACCACGCCTTCCCGGCCTCCTGACCCTTCCCAGCCCCCAGCAGGGCCAATGCAG

Alignment

ORF - retro_mmul_359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.86 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEAGAGLSETVTETTVTVTTEPENRSLTIKLRKRKPEKKVEWTSDTVDNEHMGRRSSKCCCIYEKPR-A
          MAEAGAGLSETVTETTVTVTTEPENRS.TIKLRKRKPEKKVEWTSDTVDNE.M.RRSSKCCCIYEKPR.A
Retrocopy MAEAGAGLSETVTETTVTVTTEPENRSFTIKLRKRKPEKKVEWTSDTVDNERMRRRSSKCCCIYEKPR>A

Parental  FGESSTESDEEEEEGCGHTHCVRGHRKGRRRATLGPTPTTPPQPPDPSQPPPGPMQ
          FG.SSTESDEEEEEGCGHTHCVRGHRKG.RRATLGPTPTTP..PPDPSQPP.GPMQ
Retrocopy FGDSSTESDEEEEEGCGHTHCVRGHRKGWRRATLGPTPTTPSRPPDPSQPPAGPMQ

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	44.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	47.76 RPM
SRP007412_cerebellum	0.00 RPM	33.39 RPM
SRP007412_heart	0.00 RPM	21.02 RPM
SRP007412_kidney	0.00 RPM	42.96 RPM
SRP007412_liver	0.00 RPM	20.39 RPM
SRP007412_testis	0.08 RPM	126.91 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_359 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_359 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_492

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020710	1 retrocopy	retro_cjac_2880,
Felis catus	ENSFCAG00000013592	1 retrocopy	retro_fcat_1794,
Gorilla gorilla	ENSGGOG00000026830	1 retrocopy	retro_ggor_80,
Macropus eugenii	ENSMEUG00000006493	2 retrocopies	retro_meug_715, retro_meug_933,
Macaca mulatta	ENSMMUG00000012122	1 retrocopy	retro_mmul_359 ,
Monodelphis domestica	ENSMODG00000016021	1 retrocopy	retro_mdom_98,
Nomascus leucogenys	ENSNLEG00000004933	1 retrocopy	retro_nleu_2257,
Otolemur garnettii	ENSOGAG00000001598	1 retrocopy	retro_ogar_1458,
Pteropus vampyrus	ENSPVAG00000008330	1 retrocopy	retro_pvam_894,
Ictidomys tridecemlineatus	ENSSTOG00000003632	1 retrocopy	retro_itri_159,