RetrogeneDB ID: retro_pabe_413

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:89490495..89490936(-)
• Located in intron of: ENSPPYG00000000589

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSPPYG00000008372
• Aliases: None
• Description: Proteasome activator complex subunit 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5RFD3]

Sequence

>retro_pabe_413
CTTCTGCGGAGCAACCAGCATCTGGTTGAGCTAATTGAGTGGGTGAAACCTGAGATCAAGCTGCTGAGAGAAAAATGCAG
CACAGTGCGGATGTAGGTGCACCTGCTTATCCCGAAGGTGGAGGACGGCAACAACTTCAGGGTGTCTATCCAGGAAGACA
CTGTGGACCAGCTGTGGACCGTGGAGAGCACAGCGGCCTCCTCTCTATGCGGCTTCTCCACCTACTACAACACCCGGGCC
AAGTTGGTATCCAAGATAGTGAAGTACCCCCAAGTGGAAGATTATCGCCGCACTGTAGCAGAGGTCGATGAAAACGAGTA
CCTGAGTGTGCGCCAGATCCTGCTGCACCTACGGAACCAGTATGCCACCTTGCGTGATGTAATCCTTAAAAACATCGAGA
AGATCAAGATCCCTCGGAGCACCAACAGTGATAACCTATAC

Alignment

ORF - retro_pabe_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.39 %
• Parental protein coverage: 57.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWVQLLIPRIEDGNNFGVSIQEETVAELRTVESEAASYLD
          .L.SNQ.LV..IE.VKPEI.LL.EKC.TV.M.V.LLIP..EDGNNF.VSIQE.TV..L.TVES.AAS.L.
Retrocopy LLRSNQHLVELIEWVKPEIKLLREKCSTVRM*VHLLIPKVEDGNNFRVSIQEDTVDQLWTVESTAASSLC

Parental  QISRYYITRAKLVSKIAKYPHVEDYRRTVTEIDEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPRS
          ..S.YY.TRAKLVSKI.KYP.VEDYRRTV.E.DE.EY.S.R.I...LRNQY.TL.D.ILKNIEKIK.PRS
Retrocopy GFSTYYNTRAKLVSKIVKYPQVEDYRRTVAEVDENEYLSVRQILLHLRNQYATLRDVILKNIEKIKIPRS

Parental  SNAETLY
          .N...LY
Retrocopy TNSDNLY

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	0.00 RPM	86.59 RPM
SRP007412_cerebellum	0.00 RPM	55.45 RPM
SRP007412_heart	0.09 RPM	23.72 RPM
SRP007412_kidney	0.36 RPM	70.87 RPM
SRP007412_liver	0.46 RPM	39.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_413 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_413 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_413 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_245
Pan troglodytes	retro_ptro_212
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	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413 ,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,