RetrogeneDB ID: retro_hsap_245

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:161861026..161861467(+)
• Located in intron of: ENSG00000118217

Retrocopy information

• Ensembl ID: ENSG00000229808
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSG00000131467
• Aliases: PSME3, HEL-S-283, Ki, PA28-gamma, PA28G, PA28gamma, REG-GAMMA
• Description: proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki) [Source:HGNC Symbol;Acc:9570]

Sequence

>retro_hsap_245
CTTCTGCGGAGCAACCAGCATCTGGTGGAGTTGACTGAGTGGGTGAAACCTGAGATCAAGCTGCTGAGAGAGAAATGCAA
CACAGTGCACATGTAGGTGCACCCGCTTATCCTGAAGGTGCAGGACGGCAACAACTTCAGGGTGTCTATCCAGGAAGACA
CTGTGGACCAGCTGTGGACCGTGGATAGCACAGCGGCCTCCTCTCTATGCGGCTTCTCCACCTACTACAACACCCAGGCC
AAGTTGGTATCCAAGATAGTGAAGTACCCCCAAGTGGAAGATTATCGCTGCACTGTAGCAGAGGTCGACGAAAACGAGTA
CCTGAGTGTGCGCCAGATCCTGCTGCACCTACGGAACGAGTATGCCACCTTGCGTGATGTAATCCTTAAAAACATTGAGA
AGATCAAGATCCCTCGGAGCACCAACCGTGATAACCTATAC

Alignment

ORF - retro_hsap_245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.63 %
• Parental protein coverage: 55.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWVQLLIPRIEDGNNFGVSIQEETVAELRTVESEAASYLD
          .L.SNQ.LV...E.VKPEI.LL.EKCNTV.M.V..LI....DGNNF.VSIQE.TV..L.TV.S.AAS.L.
Retrocopy LLRSNQHLVELTEWVKPEIKLLREKCNTVHM*VHPLILKVQDGNNFRVSIQEDTVDQLWTVDSTAASSLC

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

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
bodymap2_adipose	0.02 RPM	84.60 RPM
bodymap2_adrenal	0.14 RPM	93.93 RPM
bodymap2_brain	0.05 RPM	64.23 RPM
bodymap2_breast	0.04 RPM	83.52 RPM
bodymap2_colon	0.04 RPM	67.00 RPM
bodymap2_heart	0.13 RPM	47.85 RPM
bodymap2_kidney	0.14 RPM	123.40 RPM
bodymap2_liver	0.04 RPM	62.25 RPM
bodymap2_lung	0.09 RPM	50.25 RPM
bodymap2_lymph_node	1.19 RPM	62.22 RPM
bodymap2_ovary	0.10 RPM	113.77 RPM
bodymap2_prostate	0.40 RPM	72.87 RPM
bodymap2_skeletal_muscle	0.00 RPM	60.00 RPM
bodymap2_testis	0.30 RPM	101.22 RPM
bodymap2_thyroid	0.04 RPM	115.96 RPM
bodymap2_white_blood_cells	0.00 RPM	146.04 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_245 was not detected

EST

No EST(s) were mapped for retro_hsap_245 retrocopy.

TSS

No TSS is located nearby retro_hsap_245 retrocopy 5' end.

Lab

retro_hsap_245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_245 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_212
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	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
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	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,