RetrogeneDB ID: retro_cpor_920

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:488781..489115(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP3
• Ensembl ID: ENSCPOG00000001723
• Aliases: None
• Description: None

Sequence

>retro_cpor_920
GGGCTGCTTGGAAAAACCCAGGAGAAACTGCTCAAAGAGCCAGTCAGTTAATGGTCACTGAAGATAAAAAAAGAAGTAAG
AGTTGTTGGCAGGCAAGTAAGATACCCAAAAAGAAGAGAAAGTGAAACAATCTGTAGAAGATGCTATCGAGAAGGGCCAA
AGGATCCCTATGCAGTTCTCGCCAAGGAGATGATCAGGTCAGCAAAGGCTGTGAGGAAGTTCGACACATCCGAAATGCAC
AGTGACTCTGAGCACATGGGCTGAAGAACCAGCTGTGGTCTTTCAAGGGACCAGTTCTCTGCAGAAGAGCACAGTGATGA
AGGCCATGCAGTCC

Alignment

ORF - retro_cpor_920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.99 %
• Parental protein coverage: 52.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLFGKTQEKPPKEMVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQKDVCVILAKEVVRSR
          GL.GKTQEK..KE.V..WSLKI.KE.RVV.RQ.R...R.E.............G.KD....LAKE..RS.
Retrocopy GLLGKTQEKLLKEPVS*WSLKIKKEVRVVGRQVRYPKRRESET--ICRRCYREGPKDPYAVLAKEMIRSA

Parental  KAVSKLYASKAHMNSVLM-GMKNQL-AVLRVAGSLQKSTEVMKAMQS
          KAV.K...S..H..S..M.G.KNQL..V.....SLQKST.VMKAMQS
Retrocopy KAVRKFDTSEMHSDSEHM<GLKNQL<VVFQGTSSLQKST-VMKAMQS

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	40.89 RPM
SRP017611_kidney	0.00 RPM	56.22 RPM
SRP017611_liver	0.04 RPM	23.98 RPM
SRP040447_lung	0.03 RPM	63.53 RPM
SRP040447_skeletal_muscle	0.00 RPM	42.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_920 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_920 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007479	1 retrocopy	retro_cfam_1869,
Callithrix jacchus	ENSCJAG00000019406	2 retrocopies	retro_cjac_2032, retro_cjac_2784,
Cavia porcellus	ENSCPOG00000001723	1 retrocopy	retro_cpor_920 ,
Macropus eugenii	ENSMEUG00000009111	1 retrocopy	retro_meug_178,
Microcebus murinus	ENSMICG00000005492	3 retrocopies	retro_mmur_1110, retro_mmur_1396, retro_mmur_47,
Mus musculus	ENSMUSG00000053119	1 retrocopy	retro_mmus_1683,
Oryctolagus cuniculus	ENSOCUG00000029277	1 retrocopy	retro_ocun_1044,
Ochotona princeps	ENSOPRG00000002191	2 retrocopies	retro_opri_18, retro_opri_436,
Sorex araneus	ENSSARG00000008917	1 retrocopy	retro_sara_13,
Tursiops truncatus	ENSTTRG00000010400	1 retrocopy	retro_ttru_638,