RetrogeneDB ID: retro_mmul_2637

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:130355222..130356489(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000003480
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AGK
• Ensembl ID: ENSMMUG00000021017
• Aliases: None
• Description: acylglycerol kinase, mitochondrial [Source:RefSeq peptide;Acc:NP_001247490]

Sequence

>retro_mmul_2637
ATGACAGTGTAATTTAAAACACTTCAAAATCATTGGAAGAAAGCTATTGCTGGGCTCTGCCTGCTGACCTGGGGAGGTCA
GTGGCTCTATGGAAAACACTGTGATAACCTACTAAGGAGAGCAGCCTGTGAAGAAGCTCAGGTGTTTGGCAATCAACTCA
TTCCTTCCAATGCACAAGTGAAGAAGGAAACTGTTTTTCTGAATCCTGCAGCTTGCAAAGGCAAAGCCAGGACTCTATTT
GAAAAAAATGCTGCCCTGATTTTACATTTATCCTGGCATAGGTGTGACTATTGTTAAGGCAGATTATGAGGTACAAGCCA
AGAAATTCCTGGAACTGATGGAGAACACTTATGTGATCATTGTTGCAGGAGGAGATGGGACACTGCAGGAGGTTGTTACT
GGAGTTCTTCGACAAACAGATGAGGCTACCTTCAGTAAGATTCCCATTGGATTTATCCCACTGGGAGAGACCAGTAGTTT
GAGTCATAACCTCCTTACTGAAAGTGGAAGCAAACTCCAACATATTACTGATGCTACACTTGCCATTGTGAACGGAGAGA
CAGTTCCATTTGATGTCTTGCAGATCAAGGGTGAAAAGGAACAGCCTGTGTTTGCAATGACCGGTCTTTGATGGGGATCC
TTCAGAGACGCTGGCATCAAAGTTAGCAGGTACTGATATCTTGGGCCTCTAAAAATCAATGTAGCCCACTTCTTCAGCAC
TCTTAAGGAGTGGCCTCAGACTCGTGAAACCTCTATCTTGTATATGGGACCTACAGAGAGACCTCCCAATGAACCAAAGG
AGACCCCTGTACAAAGGCCTTTTTTGTACAGGAGAATATTACGAAGGCTTACATCTTACTGGGCGCAACCACAGGATGCC
CTTTCCCAAGAGGTGAGCCGAGAGATCTGGAAAGATGTGCAGCTGTCCACCATTGAACTGTCCATCACAACACAGAACAA
TCAGCTTGACCCAACACGCAAAGAAGATTTTATGAACATCTGCATTGAAGCCGACACCATCAGCAAAGGAATCTTTATAA
CTATAGGAAGTCGAAAGGTGAGAAACGCCAAGCTGGACGCCGAGGGCATGAAGTGTCTCCAAGCCAGCCAGTGCACTTTG
CTTGTCCCAGAGGGAGCAGGGAGCACTTTTAGCATTGACAGTGAGGAGTATGAAGTGATGCCTGTGGAGGTGAAACTGCT
CCCCAGGAACCTGCCGTTCTTCTGTGATCCTAGGAAGAGAGAACAGATGTTGGCAAGCCCCACTCAG

Alignment

ORF - retro_mmul_2637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVFFKTLRNHWKKTTAGLCLLTWGGHWLYGKHCDNLLRRAACQEAQEFGNQLIPPNAQVKKATVFLNPA
          MTV.FKTL.NHWKK..AGLCLLTWGG.WLYGKHCDNLLRRAAC.EAQ.FGNQLIP.NAQVKK.TVFLNPA
Retrocopy MTV*FKTLQNHWKKAIAGLCLLTWGGQWLYGKHCDNLLRRAACEEAQVFGNQLIPSNAQVKKETVFLNPA

Parental  ACKGKARTLFEKNAAPILHLS-GMDVTIVKTDYEGQAKKLLELMENTDVIIVAGGDGTLQEVVTGVLRRT
          ACKGKARTLFEKNAA.ILHLS.G..VTIVK.DYE.QAKK.LELMENT.VIIVAGGDGTLQEVVTGVLR.T
Retrocopy ACKGKARTLFEKNAALILHLS>GIGVTIVKADYEVQAKKFLELMENTYVIIVAGGDGTLQEVVTGVLRQT

Parental  DEATFSKIPIGFIPLGETSSLSHTLFAESGNKVQHITDATLAIVKGETVPLDVLQIKGEKEQPVFAMTGL
          DEATFSKIPIGFIPLGETSSLSH.L..ESG.K.QHITDATLAIV.GETVP.DVLQIKGEKEQPVFAMTGL
Retrocopy DEATFSKIPIGFIPLGETSSLSHNLLTESGSKLQHITDATLAIVNGETVPFDVLQIKGEKEQPVFAMTGL

Parental  RWGSFRDAGVKVSKYWYLGPLKIKAAHFFSTLKEWPQTHQASISYTGPTERPPSEPEETPVQRPSLYRRI
          .WGSFRDAG.KVS.Y.YLGPLKI..AHFFSTLKEWPQT...SI.Y.GPTERPP.EP.ETPVQRP.LYRRI
Retrocopy *WGSFRDAGIKVSRY*YLGPLKINVAHFFSTLKEWPQTRETSILYMGPTERPPNEPKETPVQRPFLYRRI

Parental  LRRLASYWAQPQDALSQEVSPEVWKDVQLSTIELSITTRNNQLDPTSKEDFLNICIEPDTISKGDFITIG
          LRRL.SYWAQPQDALSQEVS.E.WKDVQLSTIELSITT.NNQLDPT.KEDF.NICIE.DTISKG.FITIG
Retrocopy LRRLTSYWAQPQDALSQEVSREIWKDVQLSTIELSITTQNNQLDPTRKEDFMNICIEADTISKGIFITIG

Parental  SRKVRNPKLHAEGTECLQASRCTLLVPEGAGGSFSIDSEEYEAMPVEVKLLPRKLQFFCDPRKREQMLAS
          SRKVRN.KL.AEG..CLQAS.CTLLVPEGAG..FSIDSEEYE.MPVEVKLLPR.L.FFCDPRKREQMLAS
Retrocopy SRKVRNAKLDAEGMKCLQASQCTLLVPEGAGSTFSIDSEEYEVMPVEVKLLPRNLPFFCDPRKREQMLAS

Parental  PTQ
          PTQ
Retrocopy PTQ

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	43.14 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	44.35 RPM
SRP007412_cerebellum	0.00 RPM	36.81 RPM
SRP007412_heart	0.00 RPM	10.78 RPM
SRP007412_kidney	0.12 RPM	22.42 RPM
SRP007412_liver	0.04 RPM	8.39 RPM
SRP007412_testis	0.00 RPM	9.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2637 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2637 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4903
Pan troglodytes	retro_ptro_3269
Gorilla gorilla	retro_ggor_3061
Pongo abelii	retro_pabe_3812

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013589	1 retrocopy	retro_cjac_3228,
Gorilla gorilla	ENSGGOG00000008821	1 retrocopy	retro_ggor_3061,
Loxodonta africana	ENSLAFG00000002479	1 retrocopy	retro_lafr_403,
Microcebus murinus	ENSMICG00000002561	1 retrocopy	retro_mmur_850,
Macaca mulatta	ENSMMUG00000021017	1 retrocopy	retro_mmul_2637 ,
Mus musculus	ENSMUSG00000029916	1 retrocopy	retro_mmus_1130,
Nomascus leucogenys	ENSNLEG00000002291	1 retrocopy	retro_nleu_2349,
Pongo abelii	ENSPPYG00000018064	1 retrocopy	retro_pabe_3812,
Pan troglodytes	ENSPTRG00000019775	2 retrocopies	retro_ptro_3269, retro_ptro_3311,