RetrogeneDB ID:

retro_cpor_106

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_71:6861646..6862846(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000021609
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000006633
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_106
ATGGACAGAGCTAAAGAAAACCTCGTTTCAGGGTCTATAAAGGCCATGGGTCCTCTTGGGAACGGTCCGAAACGTGTCCT
GGTGACGCAGCAGCTTCCCTCTCAGAACCCATCATCAGGCGGCCAGGCTCAGCCGGTCTTGTGTCCTTCAAATTCCTCCC
AGCGGGTTCCTACGCAAGCGCAGAAGCTTGTCTGTAGCCAGAAGGTGGTACAGAAGCAACTGCAGGCCACCGGCAGGGCG
CACCCTGTCCCCCGGCCAGGGAACAGCACCCAGAAGCGCGAGCAGTCCCAGCTGGCAGCATCCGGAGGGAACCCTGGGAA
GGAAGTGGAATCAAAACCAAAAACTGAAGACTTGAAAAGGAGATGGTGGACTTTGGAAGATTTTGATATTGGCCGCCCGT
TAGGTAAAGGAAAGTTTGGCAATGTTTATTTGGCCAGAGAAAAACAAAGCAAGTTTATCCTGGCTCTGAAGGTGTTATTT
AAAGCCCAGCTGGAGAAAGCAGGCGTGGAGCACCAGCTCAGGAGAGAAGTGGAGATACAGTCCCACCTCCGGCATCCCAA
CATCCTCAGGCTGTACGGTTACTTACACGACGCCATGAGAGTTTACCGAATTCTGGAGTATGCCCCGCTTGGAACAGTCT
ATAGAGAACTTCAGAAACTCTCCAAGTTTGATGAGCAGAGAGCTGCTACTTATATCACGGAATTGGCAAACGTCGTGTCT
AACTGTCATTCCAAGAGAGTTATTCAAAGGGATATTAAACCAGAGAACCTGCTGCTGGGGTCAGCTGGAGAGCTGAAGAT
CGCAGATTTCGGGTGGTCAGCGCACGCTCCGTCCTCCAGGAGGACCAGTCTGTGCCGCACCCTGGACTACCAACCCCCCG
AGATGATCGAAGGCCGGAAGCATGATGAGAAGGTGGATCTCTGGAGCCTGGGCGTCCTCTGCTACAAGTTTCTGGTCGGG
AAGCCACCTTTTGAGGCGCACACGCATCAGGAGACCTACAAAAGGATCTCACAGGTCGAATTCACGTTCCCTGACTTTGT
GACAGAGGGAGCCCGGGACTTCATTTCAAGGCTGTTAAAGCAGAATCCAAGCCAGAGGCCGACTCTTAGTGAAGTCCTCG
AACACCCCTGGGTCACAACAAATTCAAGCAAGCCATCAAGTTGCCAGAAAAGCAAAGAACCAACTAGCAAATCATCTTAG

ORF - retro_cpor_106 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.82 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMDKAKENLISGSIKATGPLGNGPKRVLVMKQPPSQNPSSESSGGGQAQRVLCPSNSSQRVPTQAQKLICS
MD.AKENL.SGSIKA.GPLGNGPKRVLV..Q.PSQNPSS....GGQAQ.VLCPSNSSQRVPTQAQKL.CS
RetrocopyMDRAKENLVSGSIKAMGPLGNGPKRVLVTQQLPSQNPSS----GGQAQPVLCPSNSSQRVPTQAQKLVCS
ParentalQKVVQKQLQATGGAHPVPRPENSTQKSEQSQPAASGGNPGKEVESKPKNEDSKRRQWTLEDFDIGRPLGK
QKVVQKQLQATG.AHPVPRP.NSTQK.EQSQ.AASGGNPGKEVESKPK.ED.KRR.WTLEDFDIGRPLGK
RetrocopyQKVVQKQLQATGRAHPVPRPGNSTQKREQSQLAASGGNPGKEVESKPKTEDLKRRWWTLEDFDIGRPLGK
ParentalGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILE
GKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGY.HDA.RVY.ILE
RetrocopyGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYLHDAMRVYRILE
ParentalYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHA
YAPLGTVYRELQKLSKFDEQR.ATYITELAN..S.CHSKRVI.RDIKPENLLLGSAGELKIADFGWS.HA
RetrocopyYAPLGTVYRELQKLSKFDEQRAATYITELANVVSNCHSKRVIQRDIKPENLLLGSAGELKIADFGWSAHA
ParentalPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEAHTHQETYKRISRVEFTFPDF
PSSRRT.LC.TLDY.PPEMIEGR.HDEKVDLWSLGVLCY.FLVGKPPFEAHTHQETYKRIS.VEFTFPDF
RetrocopyPSSRRTSLCRTLDYQPPEMIEGRKHDEKVDLWSLGVLCYKFLVGKPPFEAHTHQETYKRISQVEFTFPDF
ParentalVTEGARDFISRLLKHNPSQRPTLSEVLEHPWVTTNSTKPSSCQKSKEPASKSS
VTEGARDFISRLLK.NPSQRPTLSEVLEHPWVTTNS.KPSSCQKSKEP.SKSS
RetrocopyVTEGARDFISRLLKQNPSQRPTLSEVLEHPWVTTNSSKPSSCQKSKEPTSKSS

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 1 .38 RPM
SRP017611_kidney 0 .00 RPM 0 .84 RPM
SRP017611_liver 0 .00 RPM 0 .65 RPM
SRP040447_lung 0 .00 RPM 3 .10 RPM
SRP040447_skeletal_muscle 0 .00 RPM 0 .43 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_106 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_106 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 18 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000293313 retrocopies
retro_cfam_1027, retro_cfam_257, retro_cfam_764,
Choloepus hoffmanni ENSCHOG000000059768 retrocopies
retro_chof_1302, retro_chof_1575, retro_chof_1709, retro_chof_2213, retro_chof_2389, retro_chof_259, retro_chof_565, retro_chof_764,
Cavia porcellus ENSCPOG00000006633 1 retrocopy
retro_cpor_106 ,
Felis catus ENSFCAG000000244931 retrocopy
retro_fcat_495,
Homo sapiens ENSG000000875861 retrocopy
retro_hsap_510,
Gorilla gorilla ENSGGOG000000071971 retrocopy
retro_ggor_470,
Myotis lucifugus ENSMLUG000000079251 retrocopy
retro_mluc_1931,
Macaca mulatta ENSMMUG000000000701 retrocopy
retro_mmul_431,
Mus musculus ENSMUSG000000274961 retrocopy
retro_mmus_2825,
Nomascus leucogenys ENSNLEG000000070291 retrocopy
retro_nleu_1553,
Otolemur garnettii ENSOGAG000000044413 retrocopies
retro_ogar_2805, retro_ogar_3440, retro_ogar_980,
Pongo abelii ENSPPYG000000111481 retrocopy
retro_pabe_231,
Pan troglodytes ENSPTRG000000136461 retrocopy
retro_ptro_381,
Rattus norvegicus ENSRNOG000000044792 retrocopies
retro_rnor_664, retro_rnor_670,
Sus scrofa ENSSSCG000000074931 retrocopy
retro_sscr_936,
Ictidomys tridecemlineatus ENSSTOG000000119582 retrocopies
retro_itri_366, retro_itri_772,
Tupaia belangeri ENSTBEG000000132842 retrocopies
retro_tbel_1137, retro_tbel_2604,
Tarsius syrichta ENSTSYG000000092211 retrocopy
retro_tsyr_378,


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