RetrogeneDB ID:

retro_cpor_86

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_21:2007716..2008658(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000008047
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RRAGB
Ensembl ID:ENSCPOG00000011266
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_86
ATGCCAAATACAGCCATGAAGAAAAAGGTGCTGTTGATGGGAAAGAGCGGGTCGGGGAAGACCAGCATGAGATCCATTAT
CTTTGCAAATTATATTGCTCGCGACACCAGGCGTCTGGGTGCCACCATTGATGTGGAGCACTCCCACGTCCGATTCTTAG
GGAACCTGGTGCTGAACCTGTGGGATTGTGGCGGTCAGGACACCTTTATGGAAAATTACTTCACCAGCCAGCGAGACAAC
ATCTTCCGAAATGTCGAGGTTTTGATTTACGTGTTCGATGTAGAGAGCCGCGAACTGGAAAAGGACATGCATTATTACCA
GTCATGTCTGGAGGCCATCCTCCAGAACTCACCAGATGCCAAAATCTTCTGCCTGGTGCACAAAATGGATCTAGTTCAAG
AGGATCAGCGTGACCTGATTTTTAAGGAGCGAGAGGAAGACCTGAGGCGTTTGTCTCGCCCACTGGAGTGCGCCTGTTTT
CGAACATCTATCTGGGATGAAACGCTCTACAAGGCCTGGTCTAGTATTGTCTATCAGCTGATTCCCAACGTTCAGCAGCT
GGAGATGAACCTAAGGAATTTTGCTCAAATTATTGAGGCTGATGAAGTTCTGCTGTTTGAGAGAGCGACCTTCTTGGTGA
TTTCTCATTACCAGTGCAAAGAGCAGCGTGACGTCCACCGGTTTGAAAAGATCAGCAACATTATTAAGCAATTCAAGTTG
AGCTGCAGTAAGCTGGCCGCCTCCTTTCAGAGCATGGAAGTTAGGAATTCTAACTTCGCTGCTTTCATCGACATCTTCAC
ATCAAACACGTATGTGATGGTTGTTATGTCGGATCCCTCCATCCCTTCTGCCGCTACTCTGATCAACATTCGCAATGCCA
GGAAACACTTTGAGAAGCTAGAGAGAGTGGATGGCCCCAAGCACAGTCTCCTGATGCGTTAA

ORF - retro_cpor_86 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.57 %
Parental protein coverage: 72.46 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTFDVEHSHVQFLGNLVLNLWDCGGQDSFMENYFTSQRDNIFQNVEVLIYVFDVESRELEKDMHYYQSCLE
T.DVEHSHV.FLGNLVLNLWDCGGQD.FMENYFTSQRDNIF.NVEVLIYVFDVESRELEKDMHYYQSCLE
RetrocopyTIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLE
ParentalAILQNSPDARIFCLVHKMDLVQEDQRDLIFREREEDLRRLSRPLECSCFRTSIWDETLYKAWSSIVYHLI
AILQNSPDA.IFCLVHKMDLVQEDQRDLIF.EREEDLRRLSRPLEC.CFRTSIWDETLYKAWSSIVY.LI
RetrocopyAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLI
ParentalPNVQQLEMNLRNFAEIIEADEVLLFERATFLVISHYQCKEQRDAHRFEKISNIIKQFKLSCSKLAASFQS
PNVQQLEMNLRNFA.IIEADEVLLFERATFLVISHYQCKEQRD.HRFEKISNIIKQFKLSCSKLAASFQS
RetrocopyPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQS
ParentalMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKQCLLM
MEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPK..LLM
RetrocopyMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKHSLLM

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






(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 38 .13 RPM 7 .59 RPM
SRP017611_kidney 37 .48 RPM 0 .31 RPM
SRP017611_liver 24 .38 RPM 0 .30 RPM
SRP040447_lung 40 .38 RPM 1 .08 RPM
SRP040447_skeletal_muscle 35 .40 RPM 0 .25 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_86 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_86 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 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000129201 retrocopy
Canis familiaris ENSCAFG000000165031 retrocopy
Callithrix jacchus ENSCJAG000000073171 retrocopy
Cavia porcellus ENSCPOG00000011266 1 retrocopy
retro_cpor_86 ,
Equus caballus ENSECAG000000060201 retrocopy
Felis catus ENSFCAG000000139321 retrocopy
Homo sapiens ENSG000000837501 retrocopy
Gorilla gorilla ENSGGOG000000115011 retrocopy
Loxodonta africana ENSLAFG000000161441 retrocopy
Myotis lucifugus ENSMLUG000000157201 retrocopy
Macaca mulatta ENSMMUG000000176351 retrocopy
Mustela putorius furoENSMPUG000000037301 retrocopy
Mus musculus ENSMUSG000000416581 retrocopy
Nomascus leucogenys ENSNLEG000000163501 retrocopy
Oryctolagus cuniculus ENSOCUG000000086661 retrocopy
Otolemur garnettii ENSOGAG000000003451 retrocopy
Procavia capensis ENSPCAG000000034171 retrocopy
Pongo abelii ENSPPYG000000203981 retrocopy
Pan troglodytes ENSPTRG000000219551 retrocopy
Rattus norvegicus ENSRNOG000000031601 retrocopy
Sus scrofa ENSSSCG000000298001 retrocopy



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