RetrogeneDB ID: retro_cpor_168

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:7099860..7100131(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSCPOG00000002920
• Aliases: None
• Description: None

Sequence

>retro_cpor_168
GAAGCACCTGAAGAAGAATTGGATTCCATGGCCAAGCATGAATCTAGCATGAATCAAAAGATTAAAACTCAGATAGCTCA
GGAACCAGAGCAGATTCTCAGATAACAGCAGAGGTATTGAGCCCATCTAGATTTTTCATAAAAGTATGCCTCAAGACAAG
GATATTCCCGGTTTTCCCTGTGGTGCCAAGAGAATATTTGAATTCCAGGTCATGCCACAGCTGCTCAACTACCTGAAAAC
AGACAGACTGGGCAAGAGTGTGGACTAAGGC

Alignment

ORF - retro_cpor_168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.4 %
• Parental protein coverage: 72.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAPEEELESMARHESREDNIFQKFKTQIAHEPEQILR-YGRGVEPIWISGKNIPQDKDIPDCPCGAKRIF
          EAPEEEL.SMA.HES......QK.KTQIA.EPEQILR...RG.EPI.I..K..PQDKDIP..PCGAKRIF
Retrocopy EAPEEELDSMAKHES---SMNQKIKTQIAQEPEQILR>NSRGIEPI*IFHKSMPQDKDIPGFPCGAKRIF

Parental  EFQVMPQLLNHLKADRLGTSVDWG
          EFQVMPQLLN.LK.DRLG.SVD.G
Retrocopy EFQVMPQLLNYLKTDRLGKSVD*G

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	5.81 RPM
SRP017611_kidney	0.00 RPM	5.23 RPM
SRP017611_liver	0.00 RPM	3.05 RPM
SRP040447_lung	0.00 RPM	9.31 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.53 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_168 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_168 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Cavia porcellus	ENSCPOG00000002920	1 retrocopy	retro_cpor_168 ,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,
Ictidomys tridecemlineatus	ENSSTOG00000022768	2 retrocopies	retro_itri_1348, retro_itri_1635,