RetrogeneDB ID: retro_cpor_674

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_22:2767360..2767688(-)
• Located in intron of: ENSCPOG00000014381

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT3
• Ensembl ID: ENSCPOG00000021856
• Aliases: None
• Description: None

Sequence

>retro_cpor_674
GGCGGGAAGGGGCTGCTACACAACTGTGATCCCAAATGTGAGTGTTCTGCCACATCAGGCAGGCAGGAGGCTGGCACCAA
ATTGCTGCACTGTGAGAATGAAGACCTGGTTTGTTTCTGAGATATCAAACCAATGGTACTTCATCATTACCTTGTGGTAT
GGAAGAAGCATATCAGAAATTGCAAAGATCTTAAGAGAGCTCACATAGAATTGCTTGAGAACATGGTGGCTGTTGGAAAA
AGCATCATTGAAAAGATCATTTCACAGATGTGAGGATGGGCTTTGATGTGCTGTGGTTCTGCTCCACCTCCACCTGTACC
TTTATGTT

Alignment

ORF - retro_cpor_674 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.87 %
• Parental protein coverage: 72.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPAGEPGDSDLKCVFCRIARGQEPGTELLHCENEDLVCFRDIKPAAPHHYLVVPKKHIRNCRDLGRDHIE
          G..G.....D.KC........QE.GT.LLHCENEDLVCF.DIKP...HHYLVV.KKHIRNC.DL.R.HIE
Retrocopy GGKGLLHNCDPKCECSATSGRQEAGTKLLHCENEDLVCF*DIKPMVLHHYLVVWKKHIRNCKDLKRAHIE

Parental  LVENMMTVGKTILE-KNNFTDFTDVRMGFHTPPFCSIS-HLHLHV
          L.ENM..VGK.I.E.K..FTD...VRMGF....FCS.S.HL.L.V
Retrocopy LLENMVAVGKSIIE<KDHFTD---VRMGFDVLWFCSTS<HLYLYV

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	13.00 RPM
SRP017611_kidney	0.00 RPM	9.32 RPM
SRP017611_liver	0.00 RPM	5.14 RPM
SRP040447_lung	0.00 RPM	8.75 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.73 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_674 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_674 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001830	1 retrocopy	retro_chof_38,
Callithrix jacchus	ENSCJAG00000003710	1 retrocopy	retro_cjac_3868,
Cavia porcellus	ENSCPOG00000021856	1 retrocopy	retro_cpor_674 ,
Echinops telfairi	ENSETEG00000007350	1 retrocopy	retro_etel_1567,
Macropus eugenii	ENSMEUG00000007627	1 retrocopy	retro_meug_853,
Mus musculus	ENSMUSG00000019791	1 retrocopy	retro_mmus_1387,