RetrogeneDB ID: retro_cpor_311

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:42251545..42251976(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC152
• Ensembl ID: ENSCPOG00000002761
• Aliases: None
• Description: None

Sequence

>retro_cpor_311
AGTTCAAGAATGGATCAAAGCAGAAGATGTGCAAAAAGACTAGCAGTGTGAACATTAACAAGAGTTATGAAAGATTTGCC
AAAGATAGAAAAGAAAATGATATAAACCAGTGGAAAGAGTAACAGACTGGAGATTCAGGTGGAAAAGACTTCCCATTTAT
TAAAGATAATCCAAACAAAGAAAACCTCATTTAAAAAAGAATGTGCTGCTCTTCATGATATGATAAAAGTGCTACAACAG
ACTGTCAAATATCAACACAATTGGAAAGGTGAAAATAAACAATTACAAAGAAATGATGATACGACAAAGAAAAGCTAAAA
TCTCAAGAACAAGAATATAAGAATAATATCACCAAACTTATACATGAAGTGAAAATCAAAGAGGAGGAACTTAAGATAGA
AATAAGCAAACTTTATCAAGATATGGAGAAA

Alignment

ORF - retro_cpor_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.44 %
• Parental protein coverage: 56.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSSMDQSSNECTKKISNVNIDKLIKDFSQIEKKMIETSGKNNILEIQLEKTTCLLKVIQTKETSFKKECA
          SS.MDQS...C.K...........KD...IEKKMI.TSGK.N.LEIQ.EKT..LLK.IQTK.TSFKKECA
Retrocopy SSRMDQS-RRCAKRLAV*TLTRVMKDLPKIEKKMI*TSGKSNRLEIQVEKTSHLLKIIQTKKTSFKKECA

Parental  ALHDMIKGLQQTIEYQHNLKGENEELKRNADLA-KEKLKSQEQEHMNNIAKLEYEMKIKEEQHKVEISRL
          ALHDMIK.LQQT..YQHN.KGEN..L.RN.D...KEKLKSQEQE..NNI.KL..E.KIKEE..K.EIS.L
Retrocopy ALHDMIKVLQQTVKYQHNWKGENKQLQRNDDTT<KEKLKSQEQEYKNNITKLIHEVKIKEEELKIEISKL

Parental  YQDMQK
          YQDM.K
Retrocopy YQDMEK

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	2.76 RPM
SRP017611_kidney	0.00 RPM	5.44 RPM
SRP017611_liver	0.00 RPM	20.37 RPM
SRP040447_lung	0.00 RPM	1.36 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.43 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_311 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_311 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002761	2 retrocopies	retro_cpor_311 , retro_cpor_638,
Mustela putorius furo	ENSMPUG00000014443	1 retrocopy	retro_mputfur_1496,
Otolemur garnettii	ENSOGAG00000012867	1 retrocopy	retro_ogar_1605,