RetrogeneDB ID: retro_cpor_297

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:13136304..13136678(-)
• Located in intron of: ENSCPOG00000006465

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD3
• Ensembl ID: ENSCPOG00000012304
• Aliases: None
• Description: small nuclear ribonucleoprotein D3 polypeptide 18kDa [Source:HGNC Symbol;Acc:11160]

Sequence

>retro_cpor_297
GCATTTGGTGTGCCAATTAAAGTCCTGCATGCGGCTGAGGGCTACATTGTAATATGCGAGACGAGCAATGGTGAAGTATA
CTGGAGAAGCTCGTTGAAGCAGGGGACCACATGAATTGCCAGATGTCCATCATCACAGTCAGGTACATAGATGGCTGAGT
GGCACAGCTTGAGCAGGCATACATCCATGGCGGCAAGATCTGCTTTCTGATTCTGCCTGACATGCTGAAATATGCACCCA
TGTTAAAGAGCATGAAAAATAAAAACCAAGGCTCAGGGGCTGGCCGGGGAAAAGCTGCTATTCTGAAGGCCCAAGTGACT
GCAGGAGGAAGAGGACGTGGATCAGGACGTGGAAGCATCTTCCAGAAGCAAAGA

Alignment

ORF - retro_cpor_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIGVPIKVLHEAEGHIVTCETNTGEVY-RGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQVYIRGSKIRF
          ..GVPIKVLH.AEG.IV.CET..GEVY...KL.EA.D.MNCQMS.ITV.Y.DG.VAQLEQ.YI.G.KI.F
Retrocopy AFGVPIKVLHAAEGYIVICETSNGEVY<LEKLVEAGDHMNCQMSIITVRYIDG*VAQLEQAYIHGGKICF

Parental  LILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGNIFQKRR
          LILPDMLK.APMLKSMKNKNQGSGAGRGKAAILKAQV.A.GRGRG.GRG.IFQK.R
Retrocopy LILPDMLKYAPMLKSMKNKNQGSGAGRGKAAILKAQVTAGGRGRGSGRGSIFQKQR

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	0.00 RPM	19.38 RPM
SRP017611_kidney	0.00 RPM	39.15 RPM
SRP017611_liver	0.00 RPM	30.60 RPM
SRP040447_lung	0.00 RPM	32.11 RPM
SRP040447_skeletal_muscle	0.00 RPM	44.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_297 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_297 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013864	1 retrocopy	retro_cfam_173,
Cavia porcellus	ENSCPOG00000012304	1 retrocopy	retro_cpor_297 ,
Dasypus novemcinctus	ENSDNOG00000018004	1 retrocopy	retro_dnov_2611,
Dipodomys ordii	ENSDORG00000005801	1 retrocopy	retro_dord_791,
Otolemur garnettii	ENSOGAG00000012708	3 retrocopies	retro_ogar_1209, retro_ogar_2077, retro_ogar_2235,
Rattus norvegicus	ENSRNOG00000050410	1 retrocopy	retro_rnor_232,
Ictidomys tridecemlineatus	ENSSTOG00000025674	1 retrocopy	retro_itri_651,
Tarsius syrichta	ENSTSYG00000007649	1 retrocopy	retro_tsyr_1489,
Tursiops truncatus	ENSTTRG00000006022	1 retrocopy	retro_ttru_1240,
Vicugna pacos	ENSVPAG00000000241	2 retrocopies	retro_vpac_338, retro_vpac_348,