RetrogeneDB ID: retro_cpor_802

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:6762010..6762351(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000023456
• Aliases: None
• Description: None

Sequence

>retro_cpor_802
CAGAAAATTCTCCTTGGCAGCCTCCTGATTCTGGCCACCTTCATGACTGCATGCAATGCTGAATGCTATGTCATACCTTT
GGAGAAAGTTCAAGATGGTTCACATACTGAATGCAAGGAAGTTTATGGAGTCACACACTCTTTGAAATCACATTGCAGGA
CTTTCCACTGTGATGATTGTTTGTGTGAAGAAAATGAAATAAGCTGCTGCAAATTAACTCCTATACCTGTGGACTATGAC
AGAACTATGTGCCATGTCACCTTCCACAGGAACAATGCACCTATTCTGTTATGGAGTACAGGGATCCCCAAAAGGCCTAT
GCTGTTCATACCTGGGTATTA

Alignment

ORF - retro_cpor_802 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRILLGSLLVLATFMTICNAECYVIPLEKVPDGSRTECKDLYGVTHPLKSSWRTFHCDDCYCEENEISCC
          Q.ILLGSLL.LATFMT.CNAECYVIPLEKV.DGS.TECK..YGVTH.LKS..RTFHCDDC.CEENEISCC
Retrocopy QKILLGSLLILATFMTACNAECYVIPLEKVQDGSHTECKEVYGVTHSLKSHCRTFHCDDCLCEENEISCC

Parental  KLAPVPVDYDKILCRVTFHRNN-CSYSVTEYRDPGKACVVRKWVL
          KL.P.PVDYD...C.VTFHRNN.C.YSV.EYRDP.KA..V..WVL
Retrocopy KLTPIPVDYDRTMCHVTFHRNN<CTYSVMEYRDPQKAYAVHTWVL

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	8.57 RPM
SRP017611_kidney	0.00 RPM	16.02 RPM
SRP017611_liver	0.04 RPM	4.18 RPM
SRP040447_lung	0.03 RPM	6.89 RPM
SRP040447_skeletal_muscle	0.01 RPM	8.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_802 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_802 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013377	1 retrocopy	retro_cjac_1530,
Cavia porcellus	ENSCPOG00000023456	1 retrocopy	retro_cpor_802 ,