RetrogeneDB ID: retro_cpor_415

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_148:987062..987633(-)
• Located in intron of: ENSCPOG00000007773

Retrocopy information

• Ensembl ID: ENSCPOG00000024394
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCDC122
• Ensembl ID: ENSCPOG00000003514
• Aliases: None
• Description: None

Sequence

>retro_cpor_415
GCCATGTGTAAGCAAGAAACTTCTTCATTAACTGATACTGTAGAGCAAATTGCAAAGCAACAGCAATCACAAACGTCAGA
AATAGAAAAAAAACAAACAAGCTCTGTTCCATTTACAGAATGAACTTCAGGAACTTGAAAAACAAATAGCAGCAGTCTCT
GCAGAAACTAAAGAAACAGAGAGGCAAATTTATCAGCAAGATGCTGTCATTGAGAATTCCAAACTTCAATGTGAAAGCCT
GGAAATTCAAATCAAGTCCTTACATAAAGAAAATATAAAGCTTAAATTTGATATAGAATCAGCCCAAGAAGATTTTTGTG
AACAGATGAAAAAATATAATGCATATTATGTAAAAATAAAGACACATAAAGATAATTTAGGGGAAATAGAAAGAAAATGG
TCATTTATGACTGAACTTGATGAAAAGCGAGATCTCATTAAAAAACTGAAGACAATGAAAGAGGAACTTAAGCAAGACCT
CCAAAATCCAGATGAAACAACACAAATTCAGGAAGAGATTTCAAAGCTTAAGAATGAGATTATAACTGTAAAAGAATCTA
TCATTGAAAAG

Alignment

ORF - retro_cpor_415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.81 %
• Parental protein coverage: 69.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMCKQETSSLTDTVEQIAKQQQSQTSEIEKN-KQALFHLQNELQELEKQIAAVSAETKETERQIYQQDAV
          AMCKQETSSLTDTVEQIAKQQQSQTSEI....KQALFHLQNELQELEKQIAAVSAETKETERQIYQQDAV
Retrocopy AMCKQETSSLTDTVEQIAKQQQSQTSEIXXX>KQALFHLQNELQELEKQIAAVSAETKETERQIYQQDAV

Parental  IENSKLQCESLEIQIKSLHKENIKLKFDIESAQEDFCEQMKKYNAYYVKIKTHKDNLGEIERKWSFMTEL
          IENSKLQCESLEIQIKSLHKENIKLKFDIESAQEDFCEQMKKYNAYYVKIKTHKDNLGEIERKWSFMTEL
Retrocopy IENSKLQCESLEIQIKSLHKENIKLKFDIESAQEDFCEQMKKYNAYYVKIKTHKDNLGEIERKWSFMTEL

Parental  DEKRDLIKKLKTMKEELKQNLQNPDEITQIQEEISKLKNEIITVKESIITR
          DEKRDLIKKLKTMKEELKQ.LQNPDE.TQIQEEISKLKNEIITVKESII..
Retrocopy DEKRDLIKKLKTMKEELKQDLQNPDETTQIQEEISKLKNEIITVKESIIEK

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	0.06 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	0.15 RPM
SRP040447_skeletal_muscle	0.05 RPM	0.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_415 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_415 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003514	1 retrocopy	retro_cpor_415 ,