RetrogeneDB ID: retro_ptro_3269

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:132737510..132738774(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGK
• Ensembl ID: ENSPTRG00000019775
• Aliases: None
• Description: None

Sequence

>retro_ptro_3269
ATGACGGTGTTCTTTAAAACACTTCAAAATCATTGGAAGAAAACTACAGCTGGGCTCTTCCTGCTGACCTGGGGAGGCCA
GTGGCTCTATGGAAAACACTGTGATAACCTACTAAGGAGAGCAGCCTGTGAAGAAGCTCAGGTGTTTGGCAATCAACTCA
TTCCTCCCAATGCACAAGTGAAGAAGGAAACTGTTTTTCTCAATCCTGCAGCTTGCAAAGGCAAAGCCAGGATTCTATTT
GAAAAAAATGCTGCCCCGATTTTACATTTATCCCAGCATAGGTGTGACTAGTGTTAAGACAGATTATGAGGGACAAGCCA
AGAAATTCCTGGAACTGATAGAAAACACATATGTGATCATTGTTACAGGAGGAGATGGGACACTGCAGGAGGTTGTTACT
GGAGTTCTTCGATGAACAGATGAGGCTACCTTCAGTAAGATTCCCATTGGATTTATCCCACTGGGACAGACCAGTAGTTT
GAATCATAACCTCTTTACTGAAAGTGGAAACAAAGTCCAACATATTACTGATGCTACACTTGCCATTGTGAACGGAGAGA
CAGTTCCATTTGACGTCTTGCAGATCAAGGGTGAAAAGGAACAGCCTGTGTTTGCAATGACTGGCCTTTGGTGGGGATCC
CTCAGAGATGCTGGCATCAAAGTTAGCAGGTACTGATATCTTGGGCCTCTAAAAATCAAAGCAGCCCACTTTTTCAGCAC
TCTTAAGGAGTGGCCTCAGACTCATGAAACCTCTATCTTGTATACAGGAACTACAGAGAGACCTGCCAATGAACCAGAGG
AGACCCCTGTATGAAGGCCTTCTTTGTACAGGAGAATATTACGGAGGCTTGCATCTTACTGGGCACAACCACAGGATGCC
CTTTCCCAAGAGGTGAGCCGAGAGGTCTGGAAAGATGTGCAGTTGTCCACTATTGAACTGTCCATCACGACACGGAACAA
TCAGCTTGACCGAACATGCAAAGATTTTATGAACATCTGCATTGAAGCCGACACCGTCAGCAAAGGAGGCTTTATAACTA
TAGGAAGCCTAAAGGTGAGAAAAGCCAAGCTGGACACTGAGGGCATGGAGTGTCTCCAAGCCAGCCAGTACACTTTGCTT
GTCCCCAAGGGAGCAGGGAGCTCTTTTAGCATTGACAGCGAGGAGTATGAAGCGATGCCTGTGGAAGTGAAACTGCTCCC
CAGGAAGCTGCAGTTCTTCTGTGATCCTAGGAAGAAAGAACAGATGCTGGCAAGCTCCACCCAG

Alignment

ORF - retro_ptro_3269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVFFKTLRNHWKKTTAGLCLLTWGGHWLYGKHCDNLLRRAACQEAQVFGNQLIPPNAQVKKATVFLNPA
          MTVFFKTL.NHWKKTTAGL.LLTWGG.WLYGKHCDNLLRRAAC.EAQVFGNQLIPPNAQVKK.TVFLNPA
Retrocopy MTVFFKTLQNHWKKTTAGLFLLTWGGQWLYGKHCDNLLRRAACEEAQVFGNQLIPPNAQVKKETVFLNPA

Parental  ACKGKARTLFEKNAAPILHLS-GMDVTIVKTDYEGQAKKLLELMENTDVIIVAGGDGTLQEVVTGVLRRT
          ACKGKAR.LFEKNAAPILHLS....VT.VKTDYEGQAKK.LEL.ENT.VIIV.GGDGTLQEVVTGVLR.T
Retrocopy ACKGKARILFEKNAAPILHLS>SIGVTSVKTDYEGQAKKFLELIENTYVIIVTGGDGTLQEVVTGVLR*T

Parental  DEATFSKIPIGFIPLGETSSLSHTLFAESGNKVQHITDATLAIVKGETVPLDVLQIKGEKEQPVFAMTGL
          DEATFSKIPIGFIPLG.TSSL.H.LF.ESGNKVQHITDATLAIV.GETVP.DVLQIKGEKEQPVFAMTGL
Retrocopy DEATFSKIPIGFIPLGQTSSLNHNLFTESGNKVQHITDATLAIVNGETVPFDVLQIKGEKEQPVFAMTGL

Parental  RWGSFRDAGVKVSKYWYLGPLKIKAAHFFSTLKEWPQTHQASISYTGPTERPPSEPEETPVQRPSLYRRV
          .WGS.RDAG.KVS.Y.YLGPLKIKAAHFFSTLKEWPQTH..SI.YTG.TERP..EPEETPV.RPSLYRR.
Retrocopy WWGSLRDAGIKVSRY*YLGPLKIKAAHFFSTLKEWPQTHETSILYTGTTERPANEPEETPV*RPSLYRRI

Parental  LRRLASYWAQPQDALSQEVSLEVWKDVQLSTIELSITTRNNQLDPTSKEDFLNICIEPDTISKGDFITIG
          LRRLASYWAQPQDALSQEVS.EVWKDVQLSTIELSITTRNNQLD.T.K.DF.NICIE.DT.SKG.FITIG
Retrocopy LRRLASYWAQPQDALSQEVSREVWKDVQLSTIELSITTRNNQLDRTCK-DFMNICIEADTVSKGGFITIG

Parental  SRKVRNPKLHVEGTECLQASQCTLLIPEGAGGSFSIDSEEYEAMPVEVKLLPRKLQFFCDPRKREQMLTS
          S.KVR..KL..EG.ECLQASQ.TLL.P.GAG.SFSIDSEEYEAMPVEVKLLPRKLQFFCDPRK.EQML.S
Retrocopy SLKVRKAKLDTEGMECLQASQYTLLVPKGAGSSFSIDSEEYEAMPVEVKLLPRKLQFFCDPRKKEQMLAS

Parental  PTQ
          .TQ
Retrocopy STQ

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	0.02 RPM	39.13 RPM
SRP007412_cerebellum	0.00 RPM	46.71 RPM
SRP007412_heart	0.00 RPM	10.46 RPM
SRP007412_kidney	0.00 RPM	30.73 RPM
SRP007412_liver	0.00 RPM	11.13 RPM
SRP007412_testis	0.00 RPM	20.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3269 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3269 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4903
Gorilla gorilla	retro_ggor_3061
Pongo abelii	retro_pabe_3812
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,