RetrogeneDB ID:

retro_cpor_265

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_11:49108794..49110862(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IPO5
Ensembl ID:ENSCPOG00000004827
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_265
GAAACCTATGAGAATATCCCAGGCCAGTCAAAGATCACATTTCTCTTACAAGCCATCAGGAACACAACAGCTGCTGAGGA
GGCTAGACGAATGGCCACCGTCCTCCTGCGACGCCTTTTGTCCTCTGCGTTTGATGAAGTTTATCCAACTCTCCCATTGG
ATGTTCAGACTGCCATCAAGAGTGAACTGCTAATGATCATTCAGATGGAAACGCAATCTAGCATGAGGAAGAAAATTTGT
GACATTGCTGCAGAACTGGCCAGGAATTTAATAGATGAGGATGGCAACAACCAGTGGCCTGAAGGTTTGAAGTTTCTTTT
TGATTCCGTCAGCTCTCAAAACATGGGATTGCAAGAAGCTGTGCTTCACATATTCTGGAACTTTCCTGGAATTTTTGGAA
ACCAACAGCAGCACTATTTAGATGTCATCAAACGGATGTTAGTTCAGTGTATGCAAGATCAAGAACATCCATTGATCAGG
ACATTATCTGCTAGAGCCACAGCTGCATTTATACTCGAAAATGAGCACAATGTTGCTCTCTTCAAACATTTCGCTGACTT
GTTACCTGGGTTCTCACAGGCTGTAAATGACTCGTGCTACCAGAATGATGGTTCGGTCCTAAAGTCCCTTGTTGAAATCG
CAGATACTGTTCCAAAGTATTTGCATCTTCACTTGGAAGCAACTCTGCAATTAAGTCTAAAGCTGTGTGGAGACACCAGC
CTCAATAACATGCAGCGCCAGCTTGCCCTAGAAATGATCGTGACCCTCTCAGAGACTGCGGCGGCTATGTTAAGAAAACA
TACTAATATTGTTGCACAGACAGTTCCTCAGATGTTGGCGATGATGGTTGATCTGGAAGAGGATAAGGACTGGGCCAATG
CGGATGAGCTGGAGGATGACGACTTTGACAGCAACGCAGTGGCTGGTGAGAGTGATTTAGACCGGATGGCTTGTGGACTT
GGTGGAAAGCTTGTTCTGCCGATGATCAAGGAACACATTATGCAGATGCTTCAAAACCCTGACTGGAAATACCGGCATGC
AGGATTGATGGCCTTGTCTGCCATTGGCAAAAGGTGCCACCAGCAAATGGAGGGGATTCTAAATGAGATAGTCAATTTTG
TTTTACTTTTCCTTCAGGATCCTCATCCAAGAGTGAGGTATGCAGCCTGCAACGCTGTGGGATAGATGGCTACAGATTTT
GTGCCTGGTTTCCAGAAGAAATTTCATGAGAAGGTGATTGCAGCTCTGCTGCAGACCATGGAAGACCAGGGCAACCAGCG
GGTGCAGGCCCATGCTGCTGCCGCTCTCATCAACTTCACTGAAGACTGTCCCAAGACATTGCTCATCCCCATACCTGGAT
AACTTGGTGAAGCATCTGCATTCCATTATGGTGCTGAAGCTTCAGGAGTTGATTCAGAAAGGCACCAAGTTAGTTTTGAA
ACAAGTTGTGACATCCATTGCATCAGTTGCAGATACTGCAGAAGAAAAATTTGTCCCCTACTATGATTTATTTATGCCAT
CAGTTAAGCACATCGTTGAGAATGCAGTGCAGAAGGAACTCAGACTTCTGAGAGGAAAAACCATTGAATGTATCAGCCTC
ATCGGCCTGGCAGTTGGGAAGGAAAAGTTCATGCAGGATGCGTCAAATGTGATGCAGCTGTTACTGAAGACCCAGACAGA
CTTCAACGACTTGGAGGATGACCACCCTCAGATCTCTTACATGATCTCGGCCTGGGCCAGAATGTGCAAAATCCTTGGAA
AGGAATTTCAGCAGTACCTTCCAGTGGTAATGGGGCCACTCATGAAGACGGCATCCATCAAGCCTGAAGTAGCCCTGTTG
GACACCCAGGATGTGGAGAACATGAGCGATGATGATGGCTGGGAATTTGTGAACCTTGGAGATCAACAGAGTTTTGGTAT
TAAAACTGCAGGACTGGAAGAAGAATCAACTGCTTGCCAGATGTTGGTTTGCTATGCTAAGTAATTAAAGGAAGGTTTTG
TGGAATACACTGAGCAAGTCATCAAGTTGATGGTCCCTTTACTGAAATTTTACTTCCATGATGGTGTC

ORF - retro_cpor_265 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.51 %
Parental protein coverage: 63.8 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPTLPSDVQTAIKSELLMIIQME
ETYENIPGQSKITFLLQAIRNTTAAEEAR.MA.VLLRRLLSSAFDEVYPTLP.DVQTAIKSELLMIIQME
RetrocopyETYENIPGQSKITFLLQAIRNTTAAEEARRMATVLLRRLLSSAFDEVYPTLPLDVQTAIKSELLMIIQME
ParentalTQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGLREAALHIFWNFPGIFGNQQQHYL
TQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGL.EA.LHIFWNFPGIFGNQQQHYL
RetrocopyTQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGLQEAVLHIFWNFPGIFGNQQQHYL
ParentalDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFKHFADLLPGFLQAVNDSCYQNDDSVLKSL
DVIKRMLVQCMQDQEHP.IRTLSARATAAFIL.NEHNVALFKHFADLLPGF.QAVNDSCYQND.SVLKSL
RetrocopyDVIKRMLVQCMQDQEHPLIRTLSARATAAFILENEHNVALFKHFADLLPGFSQAVNDSCYQNDGSVLKSL
ParentalVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEVIVTLSETAAAMLRKHTNIVAQTIPQMLA
VEIADTVPKYL..HLEATLQLSLKLCGDTSLNNMQRQLALE.IVTLSETAAAMLRKHTNIVAQT.PQMLA
RetrocopyVEIADTVPKYLHLHLEATLQLSLKLCGDTSLNNMQRQLALEMIVTLSETAAAMLRKHTNIVAQTVPQMLA
ParentalMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
MMVDLEED.DWANADELEDDDFDSNAVAGES.LDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
RetrocopyMMVDLEEDKDWANADELEDDDFDSNAVAGESDLDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
ParentalALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTM
ALSAIG..CHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVG.MATDF.PGFQKKFHEKVIAALLQTM
RetrocopyALSAIGKRCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVG*MATDFVPGFQKKFHEKVIAALLQTM
ParentalEDQGNQRVQAHAAAALINFTEDCPKTLLI-PYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASV
EDQGNQRVQAHAAAALINFTEDCPKTLLI.PYLDNLVKHLHSIMVLKLQELIQKGTKLVL.QVVTSIASV
RetrocopyEDQGNQRVQAHAAAALINFTEDCPKTLLI>PYLDNLVKHLHSIMVLKLQELIQKGTKLVLKQVVTSIASV
ParentalADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQT
ADTAEEKFVPYYDLFMPS.KHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDAS.VMQLLLKTQT
RetrocopyADTAEEKFVPYYDLFMPSVKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASNVMQLLLKTQT
ParentalDFNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDDDGWEF
DFND.EDD.PQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQD.ENMSDDDGWEF
RetrocopyDFNDLEDDHPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDVENMSDDDGWEF
ParentalVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPLLKFYFHDDI
VNLGDQQSFGIKTAGLEE.STACQMLVCYAK.LKEGFVEYTEQV.KLMVPLLKFYFHD..
RetrocopyVNLGDQQSFGIKTAGLEEESTACQMLVCYAK*LKEGFVEYTEQVIKLMVPLLKFYFHDGV

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 2 .88 RPM 91 .68 RPM
SRP017611_kidney 3 .25 RPM 81 .45 RPM
SRP017611_liver 2 .57 RPM 61 .68 RPM
SRP040447_lung 3 .58 RPM 107 .82 RPM
SRP040447_skeletal_muscle 8 .76 RPM 356 .55 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_265 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_265 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 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000037841 retrocopy
retro_amel_3,
Bos taurus ENSBTAG000000393741 retrocopy
retro_btau_104,
Canis familiaris ENSCAFG000000055611 retrocopy
retro_cfam_452,
Choloepus hoffmanni ENSCHOG000000060611 retrocopy
retro_chof_11,
Cavia porcellus ENSCPOG00000004827 2 retrocopies
retro_cpor_265 , retro_cpor_57,
Equus caballus ENSECAG000000148081 retrocopy
retro_ecab_37,
Felis catus ENSFCAG000000256571 retrocopy
retro_fcat_24,
Homo sapiens ENSG000000651501 retrocopy
retro_hsap_57,
Gorilla gorilla ENSGGOG000000087421 retrocopy
retro_ggor_47,
Loxodonta africana ENSLAFG000000161901 retrocopy
retro_lafr_22,
Myotis lucifugus ENSMLUG000000065001 retrocopy
retro_mluc_295,
Mus musculus ENSMUSG000000306622 retrocopies
retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys ENSNLEG000000078312 retrocopies
retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus ENSOCUG000000038981 retrocopy
retro_ocun_143,
Otolemur garnettii ENSOGAG000000075701 retrocopy
retro_ogar_169,
Pongo abelii ENSPPYG000000054581 retrocopy
retro_pabe_172,
Pan troglodytes ENSPTRG000000059842 retrocopies
retro_ptro_49, retro_ptro_745,
Pteropus vampyrus ENSPVAG000000045161 retrocopy
retro_pvam_8,
Rattus norvegicus ENSRNOG000000109891 retrocopy
retro_rnor_240,
Sus scrofa ENSSSCG000000095091 retrocopy
retro_sscr_24,
Ictidomys tridecemlineatus ENSSTOG000000111641 retrocopy
retro_itri_32,


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