RetrogeneDB ID: retro_sscr_784

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:96700827..96701268(-)
• Located in intron of: ENSSSCG00000006346

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSSSCG00000017385
• Aliases: None
• Description: Sus scrofa proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki) (PSME3), mRNA. [Source:RefSeq mRNA;Acc:NM_214348]

Sequence

>retro_sscr_784
CTCCTGCGAAGCAACCAGCATCTGGTGGAGCTGATTGAGCGGGTAAAACCTGAGATCGAGCTGCTGAGAGAGAAATGCAA
CACTGTACGGATGTGGGTGCAGCTGCTCATTCCAAAGGTGGAGGACGGCAACAACTTCGGAGTGTCTATCCAAGAAGACA
CCGTGGACCAGCTGTGGACAGTAGAGAGCACAGCAGCCTCGTATCTACGCCGCTTCTCCACCTACTACAACACCCGGGCC
AAGTTGGTATCCAAGATAGTGAAATACCCCCAGGTGGAAGATTATCGTCGCACTGTAGCTGAGGTCGATGAGAACGAGTA
CCTGAGTGTGCGCCAGATCCTACTGCATGTACGGAACCAGTATGCCACCTTGCATGATGTAATTCTCAAAAACATCGAGA
AGATCAAGACCCCTCGGAGCACCAACACTGACAACCTATAC

Alignment

ORF - retro_sscr_784 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 57.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWVQLLIPRIEDGNNFGVSIQEETVAELRTVESEAASYLD
          .L.SNQ.LV..IE.VKPEI.LL.EKCNTV.MWVQLLIP..EDGNNFGVSIQE.TV..L.TVES.AASYL.
Retrocopy LLRSNQHLVELIERVKPEIELLREKCNTVRMWVQLLIPKVEDGNNFGVSIQEDTVDQLWTVESTAASYLR

Parental  QISRYYITRAKLVSKIAKYPHVEDYRRTVTEIDEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPRS
          ..S.YY.TRAKLVSKI.KYP.VEDYRRTV.E.DE.EY.S.R.I....RNQY.TLHD.ILKNIEKIK.PRS
Retrocopy RFSTYYNTRAKLVSKIVKYPQVEDYRRTVAEVDENEYLSVRQILLHVRNQYATLHDVILKNIEKIKTPRS

Parental  SNAETLY
          .N...LY
Retrocopy TNTDNLY

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
SRP014902_placenta	0.13 RPM	14.73 RPM
SRP014902_testis	0.00 RPM	26.03 RPM
SRP018288_heart	0.00 RPM	22.71 RPM
SRP018288_kidney	0.00 RPM	37.04 RPM
SRP018288_liver	0.00 RPM	29.90 RPM
SRP018288_lung	0.10 RPM	42.05 RPM
SRP018856_adipose	0.28 RPM	24.50 RPM
SRP035408_brain	0.00 RPM	43.51 RPM
SRP035408_liver	0.00 RPM	41.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_784 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_784 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_245
Pan troglodytes	retro_ptro_212
Pongo abelii	retro_pabe_413
Oryctolagus cuniculus	retro_ocun_641
Bos taurus	retro_btau_1249
Equus caballus	retro_ecab_827

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 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	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000002004	1 retrocopy	retro_sscr_302,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784 ,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,