RetrogeneDB ID: retro_ptro_3311

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:23123336..23124215(-)
• Located in intron of: ENSPTRG00000022494

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_3311
GTGACAGTATTCTTTAAAACACTTCGAAATCATTGGAAGAAAATTACAACTGGGCTCTGCCTCCTGGCCTGGGGATGTAA
TTAGCTGTATAGAAAACACTGTGATAACCTACTAAGGAGAGCAGCCTATCAAGAAGATCAGGTGTTTGGCAATCAGCTCA
TTTCTCCAAATGCACAAGTGAAGAAGGCAACTGTTTTTCTCAATCCTGCAGCTTGCAAACGCAAAGCCAGAACTCGATTT
GAAAAAAATGCTGCCCTAATTTTACATATATCCAGGATGGATATGTCTATTATTAGGGCAGGTTATGAGGAATAAGTCAA
GGAACTCCTGGAACTGATGTTAAACACAGATGTGATCGTTGTTGTAAGAGGAGATGGGACACTGAAGGAGGTTGTTACTG
GAGTTCTTCAAAGAACAGATGAGGCTACCTTCAGTAAGATTCCCATTGGATTTATCCCACTGGGACGGACCGGTAGTTTG
AGTCATACCCTCTTTGCTGAACATGGAGACAAAGTCCAACATATAACTGATGCCACATTTGCCGTTGTGAAAGAAAAGAC
AGTTCCACTTGATGTCTTGCAGATGCAAGGTGAAAAGGAATAGCCTGTGTTTGCAGTCACTGGCCTTCGATGGGGACCCT
TCAGAGATGTTGGCATCAAAGTTAGCAAGTACTGGTATCTTGCGCCTCTAAAAATCAAAGCAGCTCACTTTTTCAGCACT
CTCAAAGAGTGGCCTCAGACTCACCAAGCCTATATTTTACACACGGCACCTACAGAGAGATCTCCCAGTGAACCAGAATA
GACCCCTGTGCAAAGGCCTTCTTTTTATAGAAGAATATTACAAAGTCTTGCATCCTACTGGGCACAACCGGAGCATGCC

Alignment

ORF - retro_ptro_3311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.52 %
• Parental protein coverage: 69.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTVFFKTLRNHWKKTTAGLCLLTWGGHWLYGKHCDNLLRRAACQEAQVFGNQLIPPNAQVKKATVFLNPA
          .TVFFKTLRNHWKK.T.GLCLL.WG...LY.KHCDNLLRRAA.QE.QVFGNQLI.PNAQVKKATVFLNPA
Retrocopy VTVFFKTLRNHWKKITTGLCLLAWGCN*LYRKHCDNLLRRAAYQEDQVFGNQLISPNAQVKKATVFLNPA

Parental  ACKGKARTLFEKNAAPILHLSGMDVTIVKTDYEGQAKKLLELMENTDVIIVAGGDGTLQEVVTGVLRRTD
          ACK.KART.FEKNAA.ILH.S.MD..I....YE...K.LLELM.NTDVI.V..GDGTL.EVVTGVL.RTD
Retrocopy ACKRKARTRFEKNAALILHISRMDMSIIRAGYEE*VKELLELMLNTDVIVVVRGDGTLKEVVTGVLQRTD

Parental  EATFSKIPIGFIPLGETSSLSHTLFAESGNKVQHITDATLAIVKGETVPLDVLQIKGEKEQPVFAMTGLR
          EATFSKIPIGFIPLG.T.SLSHTLFAE.G.KVQHITDAT.A.VK..TVPLDVLQ..GEKE.PVFA.TGLR
Retrocopy EATFSKIPIGFIPLGRTGSLSHTLFAEHGDKVQHITDATFAVVKEKTVPLDVLQMQGEKE*PVFAVTGLR

Parental  WGSFRDAGVKVSKYWYLGPLKIKAAHFFSTLKEWPQTHQASISYTGPTERPPSEPEETPVQRPSLYRRVL
          WG.FRD.G.KVSKYWYL.PLKIKAAHFFSTLKEWPQTHQA.I..T.PTER.PSEPE.TPVQRPS.YRR.L
Retrocopy WGPFRDVGIKVSKYWYLAPLKIKAAHFFSTLKEWPQTHQAYILHTAPTERSPSEPE*TPVQRPSFYRRIL

Parental  RRLASYWAQPQDA
          ..LASYWAQP..A
Retrocopy QSLASYWAQPEHA

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	0.05 RPM	39.13 RPM
SRP007412_cerebellum	0.07 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_3311 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3311 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4924

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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 ,