RetrogeneDB ID: retro_cpor_392

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:3869585..3870534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHEK1
• Ensembl ID: ENSCPOG00000026175
• Aliases: None
• Description: None

Sequence

>retro_cpor_392
GCAGTTGCAGTAAAGAATGTAGATATGAAGCATGATGTAGATTGTCCAGGAAACATTAAGAAAGTGATCTGTATCACTAA
AATGTTAAATCATGAAATTTAGTGAAATTCTATGGTCACAGGAGAGAAGGCAATATCCAGAATCTATTTCTGGAGTACGG
TGGTGGGGGAGAGCTTTTTGATAGAATAGAGCCAGACATAGGCATGCCTGAACAAGATGTTCAGAGATTCTTGCATCAAC
TCATGGCAGGGGTGGTTTATTTGCGTGGTATTGGAATAACTCGCAGGAATATTAAGCCAGAAAAATCTTCTGGATAAAAG
GGATAACCTCAAAATCTCTGGCTTTGGCTTAACCACAGTGTTTTGGCATAATAATCGCGAATGTTTATTGAACAAGACAT
GTGGTATGTTACCTTAAGTTGCTTCAGAACTTCTAAAGGGAAAGGAATTTCATGCACAACCAGTTGTTTGGCCCTGTGGA
ATAGTGCTTACTGCCATGTTGGCTGGGGAATTGCCATTGGGCCAGTGACAGTTGTCAGGAATATGTTGATTGGAAAGTAA
AGAAGGCATATCTCAACCCTTGGAAAGAAATTGATTCTGCTTCACTAGTTCTGCTACATAAAATCCTAGTTGAAAATCCA
TCGATAAGGATTACCATTCCAGACATCAAAAAAGATAGATGGTATAACAAACCACTCAAGAAAGGCGCAAAGAGGCCCCA
GGTCACTTCAGGTGGTGTGTCAGAGTCTCCTAGTGGATTCTCTAAGCCTATTCACTCAAATTTGGACTTCTCTCCAGTAA
ACAGTGCTTCTAGTGAAGAAAATGTGAAGTACTCCAGTTCTCAGCCAGAATCCTGGATGGGTCTTTCTTTGTGGGAGACC
TGTCCCTCGTATATCGATAAACTGGTATAAGGGATCAGTTTTTCTCAACCTGCATGCCCCGATCATGTT

Alignment

ORF - retro_cpor_392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 67.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVAVKIVDMKRAVDCPENIKKEICINKMLNHE-NVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIGM
          AVAVK.VDMK..VDCP.NIKK.ICI.KMLNHE.N.VKFYGHRREGNIQ.LFLEY..GGELFDRIEPDIGM
Retrocopy AVAVKNVDMKHDVDCPGNIKKVICITKMLNHE<NLVKFYGHRREGNIQNLFLEYGGGGELFDRIEPDIGM

Parental  PEQDAQRFFHQLMAGVVYLHGIGITHRDIKPE-NLLLDERDNLKISDFGLATVFRHNNRERLLNKMCGTL
          PEQD.QRF.HQLMAGVVYL.GIGIT.R.IKPE.NL.LD.RDNLKIS.FGL.TVF.HNNRE.LLNK.CG.L
Retrocopy PEQDVQRFLHQLMAGVVYLRGIGITRRNIKPE>NL-LDKRDNLKISGFGLTTVFWHNNRECLLNKTCGML

Parental  PYVAPELLKRKEFHAEPVDVWSCGIVLTAMLAGELP-WDQPSDSCQEYVDWKEKKTYLNPWKKIDSAPLA
          P.VA.ELLK.KEFHA.PV.VW.CGIVLTAMLAGELP.W...S..CQEYVDWK.KK.YLNPWK.IDSA.L.
Retrocopy P*VASELLKGKEFHAQPV-VWPCGIVLTAMLAGELP>WASDS--CQEYVDWKVKKAYLNPWKEIDSASLV

Parental  LLHKILVENPSIRITIPDIKKDRWYNKPLKKGNKKVQDEDDCYKKRPGRFYLKIFL-LSMTPYVCSLSEE
          LLHKILVENPSIRITIPDIKKDRWYNKPLKKG.K..Q.........P..F...I...L...P.....SEE
Retrocopy LLHKILVENPSIRITIPDIKKDRWYNKPLKKGAKRPQVTSGGVSESPSGFSKPIHSNLDFSPVNSASSEE

Parental  NVKYSSSQPEPRTGLSLWDTCPSYIDKLVQGISFSQPACPDHM
          NVKYSSSQPE...GLSLW.TCPSYIDKLV.GISFSQPACPDH.
Retrocopy NVKYSSSQPESWMGLSLWETCPSYIDKLV*GISFSQPACPDHV

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	0.23 RPM	1.15 RPM
SRP017611_kidney	0.10 RPM	4.08 RPM
SRP017611_liver	0.30 RPM	3.22 RPM
SRP040447_lung	0.08 RPM	3.58 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_392 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_392 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	ENSCPOG00000026175	1 retrocopy	retro_cpor_392 ,
Sus scrofa	ENSSSCG00000015215	1 retrocopy	retro_sscr_859,