RetrogeneDB ID:

retro_cpor_128

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_58:9359706..9360894(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000025958
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000007879
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_128
ATGCTAGGCCCATGTCACCTCATCGTTGTCCTCCTGGCCATGACCATCTCCTGCACTGGGGCACGCCATGCGTCACTGTG
GGCGGAAAACTGCAGAAAATCAACATATCCTCCTTCCGGACCAACCTACAAAGGACCGGTTACATGGTATGTCATAAATC
TTGATTTACCACCCTATAATAGATGGCATGAATTAATGGCTGATAAGCGACCAGTGCTAAAGATCATAGTGAAGTCCATG
AAGAATATAGTAAATACACTTGTACCGAGTGGAAAAGTTATGCAGATGGTGGATCACAAGTTGCCTAAACTACTTGGCAG
ATTTCCTAGTCCTTATGAAGAGGAAATGAAGGGAATTGCAACTGTTACTAACATACCTTTAGGAGAGATCATTTTATTCA
ATATTTTTTATGAATTGTTTACTATGTGTACCTCAATAATAACCGAAGACAAGAACGGTCATCTACTACATGTTAGAAAC
TTGGATTTTGGAATATTTCTCAAGCAGAACAAAAATAATAGTAAGTCAATAATAACTGAGCAACTAAAACTTTTAACAGT
GAATTTGGACTTCCAAAGGAACAATAAAACTGTCTTTAAGGCTACAAGCTTTGCTGGCTATGTAGGCACCCTAACGGGTT
TCAAACCAAGACTATTTAGTCTCACACTAAACCAACGTTTCAGCCTACATGGTGGCTATCTGGGTATTCTTGAGTGGATT
TTAGGAAAGAAAGATGCTGCGTGGATAGGATTTATCATTAGATCAGTGCTGGAAAATGGTATAAGCTATGAAGAAGCCCA
GAAAATACTGATGAAAACCAAGTTATTGGTCCCAGTGTACTTTATTCTGGGCGGTAGCAAGTCTGGAGAAGGATGTGTGA
TTACACGAGACAGAAAAGACTCTTTGGATGTATATGAACTCAGTCCTAAACAGGGTAGATGGTTTTTGGTGCAAACAAAT
TATGATCGATGGAGAACCCCGCTATTGCATGATCATCGCAGAACACCTGCAGAGGTGTGTCTAAAACACACAACCCAAGA
GAGGCTGTCATTTGCAAGCTTATATGACGTTCTATCAACAAAACCCATTCTCAACAAGCTGACTGTGTTCACAACCTTGA
TTGATGTTACAAACAATCGATATGAAACTTACCTCCGGAATTGCCCACACCCTTGTATGGGCTGGTAA

ORF - retro_cpor_128 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.4 %
Parental protein coverage: 92.48 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalWTEDCRKSTYPPSGPTYRGPIPWYTINLDLPPYKRWHELMADKGPMLKIIVNSMKNMVNTFAPSGKVMQM
W.E.CRKSTYPPSGPTY.GP..WY.INLDLPPY.RWHELMADK.P.LKIIV.SMKN.VNT..PSGKVMQM
RetrocopyWAENCRKSTYPPSGPTYKGPVTWYVINLDLPPYNRWHELMADKRPVLKIIVKSMKNIVNTLVPSGKVMQM
ParentalVDQKLPDLLGQFSSPYEEEMKGIADITEIPLGEIIAFNIFYELFTMCTSIITEDKKGHLLHARNMDFGIF
VD.KLP.LLG.F.SPYEEEMKGIA..T.IPLGEII.FNIFYELFTMCTSIITEDK.GHLLH.RN.DFGIF
RetrocopyVDHKLPKLLGRFPSPYEEEMKGIATVTNIPLGEIILFNIFYELFTMCTSIITEDKNGHLLHVRNLDFGIF
ParentalLGWNINNNTWVITEQLKPLSVNLDFQRNNKTVFKATSFAGYVGMLTGFKPGKFSVTLNERFSLNGGYLGL
L..N.NN....ITEQLK.L.VNLDFQRNNKTVFKATSFAGYVG.LTGFKP..FS.TLN.RFSL.GGYLG.
RetrocopyLKQNKNNSKSIITEQLKLLTVNLDFQRNNKTVFKATSFAGYVGTLTGFKPRLFSLTLNQRFSLHGGYLGI
ParentalLEWILGKKDAMWIGFITRSVLENSTSYEDAKNILANTKLLAPVYFILGGNQSGEGCVITRERKDSLDIYE
LEWILGKKDA.WIGFI.RSVLEN..SYE.A..IL..TKLL.PVYFILGG..SGEGCVITR.RKDSLD.YE
RetrocopyLEWILGKKDAAWIGFIIRSVLENGISYEEAQKILMKTKLLVPVYFILGGSKSGEGCVITRDRKDSLDVYE
ParentalLDPKQGRWYLVQTNYDHWKKPLFIDDRRTPAQTCLKRTTQENLSFATLYDILSTKPVLNKLTVFTTLMDV
L.PKQGRW.LVQTNYD.W..PL..D.RRTPA..CLK.TTQE.LSFA.LYD.LSTKP.LNKLTVFTTL.DV
RetrocopyLSPKQGRWFLVQTNYDRWRTPLLHDHRRTPAEVCLKHTTQERLSFASLYDVLSTKPILNKLTVFTTLIDV
ParentalTKNHFEAYLRDCPDPCMGW
T.N..E.YLR.CP.PCMGW
RetrocopyTNNRYETYLRNCPHPCMGW

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 29 .74 RPM
SRP017611_kidney 0 .00 RPM 44 .81 RPM
SRP017611_liver 0 .00 RPM 24 .59 RPM
SRP040447_lung 0 .00 RPM 59 .40 RPM
SRP040447_skeletal_muscle 0 .00 RPM 4 .41 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_128 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_128 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 ENSCPOG00000007879 1 retrocopy
retro_cpor_128 ,




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