RetrogeneDB ID: retro_mmul_608

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:52169194..52170015(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009932
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.3948
• Ensembl ID: ENSMMUG00000006414
• Aliases: None
• Description: ATPase family, AAA domain containing 1 [Source:RefSeq peptide;Acc:NP_001244699]

Sequence

>retro_mmul_608
GTCACTTGGAGTGATATAGCAGGTTTAGATGATGTCATTACGGATCTGAAAGACACAGTCATCTTACCTATCAAAAAGAA
ACATTTGCTTGAGAATTCCAGGCTTCTGCAGCCTCCAAAAGGTGTTCTTCTCTATGGGCCTCCAGGCTGTGGTAAAACGT
TGATTGCCAAGGCCACTGCCAAAGAAGCAGGCTGTCGATTTATTAACCTTCAGCCTTCGACACTGACCGACAAGTGGTAT
GGAGAATCTCAAAAATTGGCTGCTGCTGTCTTCTCCCTTGCCATAAAACTACAACCCTCCATCATCTTTACAGATGAAAT
AGACTCCTTTCTACGAAACTGTTCAAGTTCTGACCATGAAGCTACAGCCATGATGAAAGCTCAGTTTATGAGTCTCTGGG
ATGGATTGGATACTGATCACAGCTGCCAGGTCATAGTAATGGGAGCTACCAATTGTCCTCAGGACCTTGACTCTGCTATA
ATGAGAAGAACGCCTACAAGATTTCACATCAACAAGCCTGCTTTAAAACAGAGAGAAGCAACCTGAAACTCATCTTGAAA
AATGAAAATGTGGATAGGCATGTAGACCTGCTAGAAGTGGCCCAGGAAACTGATGGCTTTTCAGGAAGTGACCTAAAAGA
GATGTGTCGAGATGCTGCCCTCCTCTGTGTTAGAGAATATGTTAATTCTACATCAGAAGAAAGCCATGATGAAGATGAAA
TTCGGCCTGTTCAACAGCAGGACCTGCATCGGGCAATTGAAAAGATGAAGAAATCAAAGGATGCAGCATTTCAGAATGTT
TTAACACATGTTTGTTTAGAT

Alignment

ORF - retro_mmul_608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.09 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTWSDIAGLDDVITDLKDTVILPIKKKHLFENSRLLQPPKGVLLYGPPGCGKTLIAKATAKEAGCRFINL
          VTWSDIAGLDDVITDLKDTVILPIKKKHL.ENSRLLQPPKGVLLYGPPGCGKTLIAKATAKEAGCRFINL
Retrocopy VTWSDIAGLDDVITDLKDTVILPIKKKHLLENSRLLQPPKGVLLYGPPGCGKTLIAKATAKEAGCRFINL

Parental  QPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFIDEIDSFLRNRSSSDHEATAMMKAQFMSLWDGLDTDH
          QPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIF.DEIDSFLRN.SSSDHEATAMMKAQFMSLWDGLDTDH
Retrocopy QPSTLTDKWYGESQKLAAAVFSLAIKLQPSIIFTDEIDSFLRNCSSSDHEATAMMKAQFMSLWDGLDTDH

Parental  SCQVIVMGATNRPQDLDSAIMRRMPTRFHINQPALKQREAI-LKLILKNENVDRHVDLLEVAQETDGFSG
          SCQVIVMGATN.PQDLDSAIMRR.PTRFHIN.PALKQREA..LKLILKNENVDRHVDLLEVAQETDGFSG
Retrocopy SCQVIVMGATNCPQDLDSAIMRRTPTRFHINKPALKQREAT<LKLILKNENVDRHVDLLEVAQETDGFSG

Parental  SDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKSKDAAFQNVLTHVCLD
          SDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKSKDAAFQNVLTHVCLD
Retrocopy SDLKEMCRDAALLCVREYVNSTSEESHDEDEIRPVQQQDLHRAIEKMKKSKDAAFQNVLTHVCLD

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	0.22 RPM	17.93 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	16.58 RPM
SRP007412_cerebellum	0.00 RPM	15.30 RPM
SRP007412_heart	0.00 RPM	13.48 RPM
SRP007412_kidney	0.00 RPM	16.20 RPM
SRP007412_liver	0.00 RPM	3.01 RPM
SRP007412_testis	0.11 RPM	76.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_608 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_608 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005296	1 retrocopy	retro_cjac_1101,
Homo sapiens	ENSG00000138138	1 retrocopy	retro_hsap_1900,
Gorilla gorilla	ENSGGOG00000026651	1 retrocopy	retro_ggor_1393,
Macaca mulatta	ENSMMUG00000006414	1 retrocopy	retro_mmul_608 ,
Nomascus leucogenys	ENSNLEG00000012135	1 retrocopy	retro_nleu_1231,
Oryctolagus cuniculus	ENSOCUG00000012082	1 retrocopy	retro_ocun_1634,
Pan troglodytes	ENSPTRG00000002717	1 retrocopy	retro_ptro_1255,
Pteropus vampyrus	ENSPVAG00000014020	1 retrocopy	retro_pvam_1080,
Rattus norvegicus	ENSRNOG00000010861	1 retrocopy	retro_rnor_2752,
Ictidomys tridecemlineatus	ENSSTOG00000006563	1 retrocopy	retro_itri_309,