RetrogeneDB ID: retro_cpor_1397

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:27154482..27155015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPSL
• Ensembl ID: ENSCPOG00000007724
• Aliases: None
• Description: None

Sequence

>retro_cpor_1397
AAGATGGCAATTCAGGTCAAGAAAAAGCTCACCACCACCACCACTGAGCCCATTAAAAGACTCTAACCCCAATGCCTGCT
CAGGGGCTCTGCAGGCTCCAAAGGATTTGGCAGAGTGTTTCAAATTATGGATGATGACAACAACAGAACCCTTGCTTTCA
AAGATGTCTGAAAGGGTTAAATGATTATACAGTGGTTATGGAAAAAGGAAGAGGCAGAAGAGCTTTTCTGCAGGTCTGAT
AAAGATGGAAATGGAATGAGAGACTTCACTGAATTTCTTCTCACATTAAGACCTCCAATGTATAGATCCAGAAGAGAGCT
AATGATGTGAGCTTTTAGAAAGTTAGACAAGACTGGAGATGGTGTAATAACAATTAAAGACCTGAGTGGAGTGTATAATG
CAAAAACACCATCCAAAGTAACCAAAGTGGAGAATGGGCAGAAGAGCACATCTTCAGGAAATTTCTAGATAATTTTGACT
CACTCTAGGACAAAGACAGATTGGTGAGCCCCGAGGAGTTCACAAACTACTAC

Alignment

ORF - retro_cpor_1397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EMAIQAKKKLTTTT-DPIERLRLQCLARGSAGIKGLSRVFRIMDDNNNRTLDFKEF-LKGLNDYAVVMEK
          .MAIQ.KKKLTTTT..PI.RL..QCL.RGSAG.KG..RVF.IMDD.NNRTL.FK...LKGLNDY.VVMEK
Retrocopy KMAIQVKKKLTTTTTEPIKRL*PQCLLRGSAGSKGFGRVFQIMDDDNNRTLAFKDV<LKGLNDYTVVMEK

Parental  -EEAEELFRRFDKDGSGTIDFNEFLLTLRPPMSRARKEVILRAFRKLDKTGDGVITIEDLRGVYNA-KHH
          .EEAEELF.R.DKDG.G..DF.EFLLTLRPPM.R.R.E....AFRKLDKTGDGVITI.DL.GVYNA.KHH
Retrocopy >EEAEELFCRSDKDGNGMRDFTEFLLTLRPPMYRSRRELMM*AFRKLDKTGDGVITIKDLSGVYNA>KHH

Parental  PK-YQNGEWTEEQVFRKFLDNFDSPYEKDGLVTPEEFMNYY
          PK..Q.GEW.EE..FRKFLDNFDS...KD.LV.PEEF.NYY
Retrocopy PK>NQSGEWAEEHIFRKFLDNFDSL*DKDRLVSPEEFTNYY

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	0.81 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.04 RPM	0.00 RPM
SRP040447_lung	0.00 RPM	3.96 RPM
SRP040447_skeletal_muscle	0.05 RPM	0.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1397 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1397 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	ENSCPOG00000007724	1 retrocopy	retro_cpor_1397 ,