RetrogeneDB ID: retro_cpor_1378

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_77:6401225..6401725(+)
• Located in intron of: ENSCPOG00000002781

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLDN10
• Ensembl ID: ENSCPOG00000003817
• Aliases: None
• Description: None

Sequence

>retro_cpor_1378
GGGTATCTACAACTGCAAGGACTTCCTTCCCATGCTGGTGCTGGACAGTTGTATCCTGGCATGTAGAGGACTGACAATTG
CGGCTATCAGCTTGGGTTTTCCTTGGTTCCCTATTTGCACTCTTTGAAACAAAGTGTACCAAAGTTGGAGGTTTAGATAA
AGCATAAGTTAAAATTGCTTGTTTAGCTAGAATTGTATTCATAATGTTAGGGCTGTGCTCACCAACCAGCTGTTCCTTGT
AAGCAAACAAAATCACCACAGAATTCTTTGATCCTCTCTTGATGGAACAAAAATGTGAATTAGGAACTTCTCTGTTTATT
CAATGGGCAGGTGCCTGACTGCGTGATTGATGGTATCTTGTTTTACTTTTCAAATCGCAATAACAAAATATCTGGAATGT
GATACACTACAAGAGGGCCACATTTATCATGTTTTCCCAGATAAAATACCATGAAAAGGAGACTGTAAATCATCTTTCAA
AACAGTTTGATAAAAATGCT

Alignment

ORF - retro_cpor_1378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.31 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSRELQGVPAMLGSGRY-IQACRGLMIAAVSLGF-FGSIFALFGMKCTKVGGSDKTKAKIACLAGIVFIL
          G...LQG.P...G.G...I.ACRGL.IAA.SLGF..GS.FALF..KCTKVGG.DK...KIACLA.IVFI.
Retrocopy GYLQLQGLPSHAGAGQL>ILACRGLTIAAISLGF>LGSLFALFETKCTKVGGLDKA*VKIACLARIVFIM

Parental  SGLCSMTGCSLYANKITTEFFDPLFVEQKYELGAALFIGWAGASLCIIGGVIFCFSISDNNKKPRYTYNG
          .GLCS.T.CSL.ANKITTEFFDPL..EQK.ELG..LFI.WAGA.L.........F.....N......Y..
Retrocopy LGLCSPTSCSL*ANKITTEFFDPLLMEQKCELGTSLFIQWAGA*LRD*WYLVLLFKSQ*QNIWNVIHYKR

Parental  ATSVMSSRTKYHGGEGDFKTTNPSKQFDKNA
          AT..M.S..KYH..E........SKQFDKNA
Retrocopy ATFIMFSQIKYHEKE---TVNHLSKQFDKNA

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	5.69 RPM	5.87 RPM
SRP017611_kidney	1.67 RPM	102.38 RPM
SRP017611_liver	1.31 RPM	2.57 RPM
SRP040447_lung	1.69 RPM	64.09 RPM
SRP040447_skeletal_muscle	0.88 RPM	0.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1378 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1378 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003817	1 retrocopy	retro_cpor_1378 ,
Echinops telfairi	ENSETEG00000005415	1 retrocopy	retro_etel_1660,