RetrogeneDB ID: retro_pabe_3812

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:131556853..131558117(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGK
• Ensembl ID: ENSPPYG00000018064
• Aliases: AGK, MULK
• Description: Acylglycerol kinase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5RED7]

Sequence

>retro_pabe_3812
ATGACGGTGTTCTTTAAAACACTTCAAAATCATTGGAAGAAAACTACAGCTGGGCTCTTCCTGCTGCCCTGGGGAGGCCA
GCGGCTCTATGGAAAACACTGTGATAACCTACTAAGGAGAGCAGCCTGTGAAGAAGCTCAGGTGTTTGGCAATCAACTCA
TTCCTCCCAATGCACAAGTGAAGAAGGAAACTGTTTTTCTCAATCCTGCAGCTTGCAAAGGCAAAGCCAGGATTCTATTT
GAAAAAAATGCTGCCCCGATTTTACATTTATCCCGGCATAGGTGTGACTATTGTTAAGACAGATTATGAGGGACAAGCCA
AGAAATTCCTGGAACTGATAGAAAACACATATGTGATCATTGTTGAAGGAGGAGATGGGACACTGCAAGAGGCTGCTACT
GGAGTTCTTTGATGAACAGATGAGGCTACCTTCAGTAAGATTCCCATTGGATTTATCCCACTGGGAGAGACCGGTAGTTT
GAGTCATAACCTCTTTACTGAAAGTGGAAACAAAGTCCAACATATTACTGATGCTACACTTGCCATTGTGAACGGAGAGA
TAGTTCCATTCGATGTCTTGCAGATCAAGGGTGAAAAGGAACAGCCTGTGTTTGCGATGACCGGCCTTTGATGGGGATCC
TTCAGAGATGCTGGCATCAAAGTTAGCAGGTACTGATATCTTGGGCCTCTAAAAATCAAAGCAGCCCACTTTTTCAGCAC
TCTTAAGGAGTGGCCTCAGACTCATGAAACCTCTATCTCGTATACAGGACCTACAGAGAGACGTGCCAATGAACCAGAGA
AGACCCCTGTATGAAGGCCTTCTTTGTACAGGAGAATATTACGGAGGCTTGCATCTTACTGGGCACAACCACAGGATGCC
CTTTCCCAAGAGGTGAGCGGAGAGGTCTGGAAAGATGTGCAGTTGTCCACCATTGAACTGTCCATCACAACACGGAACAA
TCAGCTTGACGGAACACGCAAAGATTTTATGAACATCTGCATTGAAGCCGACACCGTCAGCAAAGGAGGCTTTATAACTA
TACGAAGTCTAAAGGTGAGAAAAGCCAAGCTGGACACCGAGGGCATGGAGTGTCTCCAAGCCAGCCAGTACACTTTGCTT
GTCCCCGAGGGAGCAGGGAGCTCTTTTAGCATTGACAGTGAGGAGTATGAAGCGATGCCTGTGGAGGTGAAACTGCTCCC
CAGGAAGCTGCAGTTCTTCTGTGATCCTAGGAAGAGAGAACAGATGCTGGCAAGCCCCACCCAG

Alignment

ORF - retro_pabe_3812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVFFKTLRNHWKKTTAGLCLLTWGGHWLYGKHCDNLLRRAACQEAQVFGNQLIPPNAQVKKATVFLNPA
          MTVFFKTL.NHWKKTTAGL.LL.WGG..LYGKHCDNLLRRAAC.EAQVFGNQLIPPNAQVKK.TVFLNPA
Retrocopy MTVFFKTLQNHWKKTTAGLFLLPWGGQRLYGKHCDNLLRRAACEEAQVFGNQLIPPNAQVKKETVFLNPA

Parental  ACKGKARTLFEKNAAPILHLC-GMDVTIVKTDYEGQAKKLLELMENTDVIIVAGGDGTLQEVVTGVLRRT
          ACKGKAR.LFEKNAAPILHL..G..VTIVKTDYEGQAKK.LEL.ENT.VIIV.GGDGTLQE..TGVL..T
Retrocopy ACKGKARILFEKNAAPILHLS>GIGVTIVKTDYEGQAKKFLELIENTYVIIVEGGDGTLQEAATGVL**T

Parental  DEATFSKIPIGFIPLGETSSLSHTLFAESGNKVQHITDATLAIVKGETVPLDVLQIKGEKEQPVFAMTGL
          DEATFSKIPIGFIPLGET.SLSH.LF.ESGNKVQHITDATLAIV.GE.VP.DVLQIKGEKEQPVFAMTGL
Retrocopy DEATFSKIPIGFIPLGETGSLSHNLFTESGNKVQHITDATLAIVNGEIVPFDVLQIKGEKEQPVFAMTGL

Parental  RWGSFRDAGVKVSKYWYLGPLKIKAAHFFSTLKEWPQTHQASISYTGPTERPPSEPEETPVQRPSLYRRI
          .WGSFRDAG.KVS.Y.YLGPLKIKAAHFFSTLKEWPQTH..SISYTGPTER...EPE.TPV.RPSLYRRI
Retrocopy *WGSFRDAGIKVSRY*YLGPLKIKAAHFFSTLKEWPQTHETSISYTGPTERRANEPEKTPV*RPSLYRRI

Parental  LRRLASYWAQPQDALSQEVSPEVWKDVQLSTIELSITTRNNQLDPTSKEDFLNICIEPDTISKGDFITIG
          LRRLASYWAQPQDALSQEVS.EVWKDVQLSTIELSITTRNNQLD.T.K.DF.NICIE.DT.SKG.FITI.
Retrocopy LRRLASYWAQPQDALSQEVSGEVWKDVQLSTIELSITTRNNQLDGTRK-DFMNICIEADTVSKGGFITIR

Parental  SRKVRNPKLHAEGTECLQASQCTLLIPEGAGGSFSIDSEEYEAMPVEVKLLPRKLQFFCDPRKREQMLTS
          S.KVR..KL..EG.ECLQASQ.TLL.PEGAG.SFSIDSEEYEAMPVEVKLLPRKLQFFCDPRKREQML.S
Retrocopy SLKVRKAKLDTEGMECLQASQYTLLVPEGAGSSFSIDSEEYEAMPVEVKLLPRKLQFFCDPRKREQMLAS

Parental  PAQ
          P.Q
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_prefrontal_cortex	0.06 RPM	30.58 RPM
SRP007412_cerebellum	0.00 RPM	46.82 RPM
SRP007412_heart	0.00 RPM	7.01 RPM
SRP007412_kidney	0.00 RPM	17.83 RPM
SRP007412_liver	0.00 RPM	9.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3812 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3812 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
Macaca mulatta	retro_mmul_2637

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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,