RetrogeneDB ID: retro_cpor_436

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:40927944..40928484(-)
• Located in intron of: ENSCPOG00000000591

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSCPOG00000001046
• Aliases: None
• Description: None

Sequence

>retro_cpor_436
ATTCAGGGTGGAGACTTCTCAAATCAGAATGGAACAGGTGGAGAAAGGATTCATGCAAAAAGTTTGAAGATGAAAACTTT
CACCACAAGCATGACCACAAGGGTTCACCCAGCAAGGCAAAGGCAGGGCGGAGACAAAGGCTTCTCAGTTCTGTATCACC
ACAGCCCCAGCCCCTCGTTTGGCAGGGAAATGGGTGGCGCTTGGCCAAGCAATTGAAGAAATAGGTGTGGTGAGGATACT
GGAAAACGGAGAGGCAAATGGGGAAGTTACGACGGAAAGTGGAGAACTGCAAGAAGGTGACGACGGGGGAAATGTTCCCA
AAAGATGGCTCTGTTGCAGTCATCCAGATGTCCCTGACAACTCTGATATGGATTTCAAAGATGTAGATAGAATTTTATTA
ACAACAGAAGACATAGAACATTGGAAATACCCTTTTTTACATCTCAGAACTGGAAGATATCCACTAGAAAAATACACAAA
GGTCTTCAGGTGTATGGATTGCTCAGAGCTGTTATTAAGGAAGCAGACAGACTCAGGCTG

Alignment

ORF - retro_cpor_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.21 %
• Parental protein coverage: 50.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IQGGDFSNQNGTGGESIYGE-KFEDENFHYKHDREGLLSMANAG-PNTNGSQFFITTVPTPHLDGKHVVF
          IQGGDFSNQNGTGGE.I....KFEDENFH.KHD..G..S.A.AG...T..SQF.ITT.P.P.L.GK.V..
Retrocopy IQGGDFSNQNGTGGERIHAK<KFEDENFHHKHDHKGSPSKAKAG<AETKASQFCITTAPAPRLAGKWVAL

Parental  GQVIKGIGVARLLENVEVNGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDCHPDFPEDSDVDFKDVDKI
          GQ.I..IGV.R.LE....NGE......V..E.GEL.EGDD.G..PK......HPD.P..SD.DFKDVD.I
Retrocopy GQAIEEIGVVRILE----NGEANGE--VTTESGELQEGDDGGNVPKRWLCCSHPDVPDNSDMDFKDVDRI

Parental  LLITEDL-KNLGNTFFKSQNWEMA-IKKYRKVLRYVDSS-KAILPEAAAPRL
          LL.TED....L...FF.SQNW......KY.KV.R..D.S..A...EA...RL
Retrocopy LLTTEDI<RTLEIPFFTSQNWKIS>LEKYTKVFRCMDCS<RAVIKEADRLRL

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	34.86 RPM
SRP017611_kidney	0.00 RPM	31.30 RPM
SRP017611_liver	0.00 RPM	42.53 RPM
SRP040447_lung	0.08 RPM	21.01 RPM
SRP040447_skeletal_muscle	0.00 RPM	41.92 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_436 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_436 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001046	2 retrocopies	retro_cpor_275, retro_cpor_436 ,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,