RetrogeneDB ID: retro_ptro_212

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:140144831..140145272(+)
• Located in intron of: ENSPTRG00000001596

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSPTRG00000009225
• Aliases: None
• Description: Pan troglodytes proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki) (PSME3), mRNA. [Source:RefSeq mRNA;Acc:NM_001251895]

Sequence

>retro_ptro_212
CTTCTGCGGAGCAACCAGCATCTGGTGGAGCTGACTGAGTGGGTGAAACCTGAGATCAAGCTGCTGAGAGAAAAATGCAA
CACAGTGCAGATGTAGGTGCACCCGCTTATCCTGAAGGTGGAGGACGGCAACAACTTCAGGGTGTCTATCCAGGAAGACA
CTGTGGACCAGCCGTGGACCGTGGAGAGCACAGCGGCCTCCTCTCTATGCGGCTTCTCCACCTACTACAACACCTAGGCC
AAGTTGGTATCCAAGATAGTGAAGTACCCCCAAGTGGAAGATTATCGCTGCACTGTAGCAGAGGTCGACGAAAACGAGTA
CCTGAGTGTGTGCCAGATCCTGCTGTACCTACGGAACGAGTATGCCACCTTGCGTGATGTAATCCTTAAAAACATCGAGA
AGATCAAGATCCCTCGGAGCACCAACCGTGATAACCTATAC

Alignment

ORF - retro_ptro_212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.63 %
• Parental protein coverage: 57.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWVQLLIPRIEDGNNFGVSIQEETVAELRTVESEAASYLD
          .L.SNQ.LV...E.VKPEI.LL.EKCNTV.M.V..LI...EDGNNF.VSIQE.TV....TVES.AAS.L.
Retrocopy LLRSNQHLVELTEWVKPEIKLLREKCNTVQM*VHPLILKVEDGNNFRVSIQEDTVDQPWTVESTAASSLC

Parental  QISRYYITRAKLVSKIAKYPHVEDYRRTVTEIDEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPRS
          ..S.YY.T.AKLVSKI.KYP.VEDYR.TV.E.DE.EY.S...I...LRN.Y.TL.D.ILKNIEKIK.PRS
Retrocopy GFSTYYNT*AKLVSKIVKYPQVEDYRCTVAEVDENEYLSVCQILLYLRNEYATLRDVILKNIEKIKIPRS

Parental  SNAETLY
          .N...LY
Retrocopy TNRDNLY

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	0.13 RPM	60.34 RPM
SRP007412_cerebellum	0.11 RPM	67.36 RPM
SRP007412_heart	0.20 RPM	36.52 RPM
SRP007412_kidney	0.39 RPM	70.22 RPM
SRP007412_liver	0.59 RPM	58.69 RPM
SRP007412_testis	0.32 RPM	93.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_212 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_212 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_212 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_245
Pongo abelii	retro_pabe_413
Oryctolagus cuniculus	retro_ocun_641
Bos taurus	retro_btau_1249
Sus scrofa	retro_sscr_784
Equus caballus	retro_ecab_827

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013688	2 retrocopies	retro_acar_118, retro_acar_37,
Bos taurus	ENSBTAG00000019918	2 retrocopies	retro_btau_1249, retro_btau_941,
Callithrix jacchus	ENSCJAG00000013111	1 retrocopy	retro_cjac_2307,
Cavia porcellus	ENSCPOG00000012552	1 retrocopy	retro_cpor_1204,
Equus caballus	ENSECAG00000012620	2 retrocopies	retro_ecab_29, retro_ecab_827,
Homo sapiens	ENSG00000131467	1 retrocopy	retro_hsap_245,
Loxodonta africana	ENSLAFG00000013446	1 retrocopy	retro_lafr_725,
Mustela putorius furo	ENSMPUG00000010027	1 retrocopy	retro_mputfur_619,
Oryctolagus cuniculus	ENSOCUG00000015986	1 retrocopy	retro_ocun_641,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212 ,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,