RetrogeneDB ID: retro_cpor_1204

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_56:11485642..11486083(+)
• Located in intron of: ENSCPOG00000010325

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSCPOG00000012552
• Aliases: None
• Description: None

Sequence

>retro_cpor_1204
CTGCTTCGGAGCAATCAGCATCTCGTGGAGTTGATTGAGCGGGTCAAGCCTGAGATTGAGCTGTTGAGAGAGAAGTGCAA
CACGGTGCGCATGTGGGTCCAGCTGCTCATCCCAAAGGTGGAGGACGGCAATAACTTTGGAGTGTCTATCCAGGAGGACA
CCGTAGACCAGCTGTGGACTGTGGAGAGCACTGCCACCTCCTATCTACGCCGCTTCTCCACCTACTATAACACCCGGGCC
AAGTTGGTGTCCAAGTTAGTGAAGTACCCTCAAGTGGAAGATTATCTCCGCACCATAGCGGAGGTCGACGAAAATGAGTA
CCTGAGTGTGCGCCAGATCTTAGTGCACGTCCGGAACCAGTATGCTACCTTGCATGATGTCATCCTCAAGAACATGGAGA
AGATCAAGACCCCGCGGAGCACCAACACTGACAACCTGTAC

Alignment

ORF - retro_cpor_1204 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.39 %
• 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.A.SYL.
Retrocopy LLRSNQHLVELIERVKPEIELLREKCNTVRMWVQLLIPKVEDGNNFGVSIQEDTVDQLWTVESTATSYLR

Parental  QISRYYITRAKLVSKIAKYPHVEDYRRTVTEIDEKEYISLRLIISELRNQYVTLHDMILKNIEKIKRPRS
          ..S.YY.TRAKLVSK..KYP.VEDY.RT..E.DE.EY.S.R.I....RNQY.TLHD.ILKN.EKIK.PRS
Retrocopy RFSTYYNTRAKLVSKLVKYPQVEDYLRTIAEVDENEYLSVRQILVHVRNQYATLHDVILKNMEKIKTPRS

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
SRP017611_brain	0.12 RPM	48.08 RPM
SRP017611_kidney	0.52 RPM	44.49 RPM
SRP017611_liver	0.00 RPM	31.60 RPM
SRP040447_lung	0.23 RPM	45.93 RPM
SRP040447_skeletal_muscle	0.08 RPM	40.09 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1204 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1204 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 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	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,