RetrogeneDB ID: retro_cpor_1101

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_46:872240..872414(-)
• Located in intron of: ENSCPOG00000011050

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMA7
• Ensembl ID: ENSCPOG00000027460
• Aliases: None
• Description: None

Sequence

>retro_cpor_1101
GGTGGCAAGAAGCCCCTAACACAGCCCAAGAAGTACACCAAGGAGATGGATGAAGGAGAAAAGGCTTTCAAGCAGAAGCA
AAATGAGGAGCAAAAGAAACTCAAGGAGCTAGATAAGAAAGTTGTTGAGAAGGACCACCTGGTCAGAGGTGGAACTTAAA
AATCTGGCAAAAAG

Alignment

ORF - retro_cpor_1101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.41 %
• Parental protein coverage: 90.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKKKPLKQPKKQAKEMDEEDRAFKQKQKEEQKKLEELKTKAAGKGPLAATGGIKKSGKK
          G.KKPL.QPKK..KEMDE...AFKQKQ.EEQKKL.EL..K...K..L...GG..KSGKK
Retrocopy GGKKPLTQPKKYTKEMDEGEKAFKQKQNEEQKKLKELDKKVVEKDHL-VRGGT*KSGKK

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	13.23 RPM
SRP017611_kidney	0.00 RPM	24.18 RPM
SRP017611_liver	0.04 RPM	18.67 RPM
SRP040447_lung	0.03 RPM	15.56 RPM
SRP040447_skeletal_muscle	0.01 RPM	9.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1101 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1101 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027460	4 retrocopies	retro_cpor_1101 , retro_cpor_1380, retro_cpor_141, retro_cpor_199,