RetrogeneDB ID:

retro_cpor_62

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_1:24735335..24736289(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000013419
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000026920
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_62
ATGAATTTGGGGAGTCTAACTACATGGAATCAAACTTCAAGCACTGACTTCATCCTTGTGGGGCTCTTCATGGACACCAA
GCATGCCGCTTTGCTCTACACCATGATCTTCATATTCTTCTTGCTGGCTCTGGCCAGCAGTGCCATTCTCATTGCCCTGA
TCCACTTGGACCTCTGCCTCCACACGCCCATGTACTTCCTCCTCAGCCAGCTGTCACTCATGGACCTCCTAAACATATCC
ATCACGGTGCCCAAGATGCTTGTGGGCCAGGTCACTGGAGATCACACAATTTCCCCCTTGGGCTGTGAGATCCAGATGTC
CTTTTACCTGACCCTGGCTGGGGCTGAGTTCTTCCTCCTAGGAGTGATGGCCTATGACAAATATGCTGCCATTTGCAGGC
CTCTCCACTACCTACTACTGATGAGCCCAAGGGTGTGCCGACTGCTGGCGGACAGTTCCCGGTGTGTGGGGATACTGGAT
GCCCTGCTGATCGCCCTCATCACCCTGAGCTTCCCCTACTGTCAGTCTAGGAGAATCCTGAGCTTCTTCTGTGAAGCCCC
CGCCCTGCTCAAGCTCTCCTGCTCTGACATCTGCCTCTACAGCTTGCTCATGTACTTGTGCTGCGTGCTCATGATCCTGG
TCCCCATCCTGGTCACTTTGGGCTCCTACACCCTGATCCTGTGCCTCATCCAAAGGACGAACTCAGCCAAAGGCCCCAGC
GAGGCCTTTGCCACCTGCTCCTCACACATAATCGTGGTGGTGCTATTCTATGGAGCCACCCTCTATTTCTACATCCTTCC
CAGCCCCTACCACACAGCCCGGCAGGACATGATGGGGTCTGCCTTGTATACAATCATCACGCCAGTGCTGAACCCTCTCA
TCTACAGCCTGCAGAACAAGGATGTCGCAAGGGCCCTGAGCAGCATGGTTCAGCCAAGAGCGAGCTTCAGGAGT

ORF - retro_cpor_62 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.29 %
Parental protein coverage: 97.78 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGSLTPWNQTLSTDFILVGLFMDTKHAALLYTVIFIFFLLALARSALFSVLIHLDLHLHRLMYFLLSQLSL
GSLT.WNQT.STDFILVGLFMDTKHAALLYT.IFIFFLLALA.SA....LIHLDL.LH..MYFLLSQLSL
RetrocopyGSLTTWNQTSSTDFILVGLFMDTKHAALLYTMIFIFFLLALASSAILIALIHLDLCLHTPMYFLLSQLSL
ParentalMDLLYMPVTVPEILVSQVTGDHTISPSGCGIQIFFYLTQAGAKFFHLGAMAYDQYAAICRPLHYPLLMNH
MDLL....TVP..LV.QVTGDHTISP.GC.IQ..FYLT.AGA.FF.LG.MAYD.YAAICRPLHY.LLM..
RetrocopyMDLLNISITVPKMLVGQVTGDHTISPLGCEIQMSFYLTLAGAEFFLLGVMAYDKYAAICRPLHYLLLMSP
ParentalRACLLLTTGCWFLGSVDGFMLTSVTMTFPFCGSQEFHHFFCEVPAVTKLSCSDTSLYKTLMYLCCVLMIL
R.C.LL.......G..D.......T..FP.C.S.....FFCE.PA..KLSCSD..LY..LMYLCCVLMIL
RetrocopyRVCRLLADSSRCVGILDALLIALITLSFPYCQSRRILSFFCEAPALLKLSCSDICLYSLLMYLCCVLMIL
ParentalNPVIVISSSYTSILLTILRMNLEEGWKKALATCSSHMTVVLLFYGVAVYTYMLSSSYHTPQKNMVDSVFY
.P..V...SYT.IL..I.R.N...G...A.ATCSSH..VV.LFYG...Y.Y.L.S.YHT....M..S..Y
RetrocopyVPILVTLGSYTLILCLIQRTNSAKGPSEAFATCSSHIIVVVLFYGATLYFYILPSPYHTARQDMMGSALY
ParentalTILTPVLNTLIYSFRNKDVTEALNILPQ
TI.TPVLN.LIYS..NKDV..AL....Q
RetrocopyTIITPVLNPLIYSLQNKDVARALSSMVQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 0 .00 RPM
SRP017611_kidney 0 .00 RPM 0 .00 RPM
SRP017611_liver 0 .00 RPM 0 .00 RPM
SRP040447_lung 0 .00 RPM 0 .00 RPM
SRP040447_skeletal_muscle 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_62 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_62 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG00000026920 1 retrocopy
retro_cpor_62 ,




Copyright © RetrogeneDB 2014-2017