RetrogeneDB ID: retro_cpor_379

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:1980589..1980850(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000006809
• Aliases: None
• Description: None

Sequence

>retro_cpor_379
GGGAATGAGGGTGTCTTGCTGGCTAACACTGACACACATGCTTTCTGTACAGACATCCCACCTACCACCGCAGTGGACTT
GATTGGAAGATGTTATTTCACCGAAATCTGCAAGTGTAAACTGAAAGACATCTTGTGTTTAAAATGTGGAAACGTTGTAG
GTTATCCGGGGATTGTTCCCTGTAGTTCCTGCCTTCTTTCCTGCAACTATAAACACTTCTGAATGTTTCACAATCAGGCA
GTTCCTGGTATACACTTCCTA

Alignment

ORF - retro_cpor_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 58.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GMKAVLLADTEIDLFSTDIPPTNAVDFIGRCYFTEICKCKLKDIACLKCGNIVGYHVIVPCSSCLLSCNN
          G...VLLA.T....F.TDIPPT.AVD.IGRCYFTEICKCKLKDI.CLKCGN.VGY..IVPCSSCLLSCN.
Retrocopy GNEGVLLANTDTHAFCTDIPPTTAVDLIGRCYFTEICKCKLKDILCLKCGNVVGYPGIVPCSSCLLSCNY

Parental  GHFWMFHSQAVYGINRL
          .HF.MFH.QAV.GI..L
Retrocopy KHF*MFHNQAVPGIHFL

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	0.58 RPM
SRP017611_kidney	0.00 RPM	0.21 RPM
SRP017611_liver	0.00 RPM	0.04 RPM
SRP040447_lung	0.00 RPM	0.38 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_379 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_379 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006809	2 retrocopies	retro_cpor_379 , retro_cpor_391,