RetrogeneDB ID:

retro_cpor_57

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_21:14041342..14044657(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000005398
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:IPO5
Ensembl ID:ENSCPOG00000004827
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_57
ATGGCGGCGGCCGGTTCTGTAGGAGTACCGGGGACCGTGTCGGAAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTGAT
AAACCCAAGCTGTATGGTGCGGAGGCAAGCAGAGGAAATCTATGAAAACATACCAGGTCTGTGTAAGACTACCTTTCTAT
TAGATGCAGTCAGAAACAGAAGAGTAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGTTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAGGTCTATCCAAATCTGCCTTTTGATGTTCAGAGGGATGTCAAGATTGAACTGATACTGGCTGTTAAGTT
AGAAACACATACTAGCATGAGGAAAAAGCTTTGTGATATTTTTGCTGTGCTGGCTAGGAATTTGATAGATGAGGATGGCA
CTAATCATTGGCCAGAAGGTCTGAAGTTCCTTATTGATTCGATCTACTCTAAAAATGTAGTTCTATGGGAAGTTGCACTT
CATGTCTTCTGGCACTTTCCTGGGATTTTTGGGAACCAAGATCGACACGATTTGGATATCATCAAAAGGTTGTTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACATTATCTGCTAGAGCTGCAGCTGCATTCGTACTTGCTAATGAAA
ATAATATTGCACTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTGAATGATTCATGCTACCAGGAT
GATGATTCAGTACTAGAGTCTCTTGTTGAGATTGCAGATACTGTACCTAAGTACTTGGGTCCTTATATAGAAGATACTCT
ACAATTGAGCCTGAAGTTATGTGGAGACTCTAGACTTAGTAATCTACAACGCCAGTTGGCTCTTGAAGTGATAGTAACCT
TGTCTGAAACTGCAACTCCAATGTTGAAAAAACATACAAATATTATTGCACAGGCAGTTCCTCATATATTAGCAATGATG
GTTGAGCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
TGAGAGTGCGCTAGACAGGCTGGCTTGTGGGCTTGGTGGAAAAATTGTTTTACCAATGACCAAAGAGCATATCATGCAAA
TGCTTCAGAGCCCTGACTGGAAATGTCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGTTGCCATCAGCAA
ATGGAACCAATTCTAGATGAAACAGTAAACTCTGTTTTGCTTTTTCTTCAGGATCCTCACCCAAGGGTGAGGGCTGCAGC
CTGTACTACTCTTGGACAGATGGCTACAGATTTTGCACCTAGTTTCCAAAAGAAATTCCATGAAACAGTGATTGCAGCTT
TATTACGTACTATGGAAAATCAAGGTAATCAGCGTGTGCAGTCTCATGCAGCTTCTGCCCTTATTATTTTTATTGAAGAC
TGTCCTAAATCACTGCTAGTTCTATATTTGGATGGTATGGTAAAAAATCTACATTCCATCTTGGTGATTAAACTTCAAGA
GCTGATTCGAAATGGTACTAAGTTGGCATTAGAACAACTTGTGACAACTATTGCCTCAGTTGCAGATACAATGGAAGAAA
AATTTGTTCCATATTATGATACATTTATGCCCTCACTAAGACACATTGTTGAGCTTGCTGTTCAGAAGGACCTCAAGACT
TTGAGAGGAAAGACTATTGAGTGCATTAGCCACGTTGGTCTTGCTGTTGGAAAGGAAAAATTTATGCAAGATATATCAAA
TGTGATGGAGCTATTGTTGAAGGCACAGTCAGACTTAAGTAATATAGAAGATGATGACCCTCAGACATCATATATGGTTT
CAGCATGGGCTAGAATGTGTAAAATTCTTGGAAAAGATTTTCAACAGTATCTTCCACTAGTTATTGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTGGCTCTCTTAGATACACAAGATGTGGAGAATATGAGTGATGATGATGGTTGGCAATT
TGTAAATCTTGGAGATCAGCAAAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAGATGTTGG
TTTACTACGCTAAGGAATTAAGAGAAGGATTTGTAGAATATACAGAACAAGTTGTTAAACTGATGATTCCTTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTAGCAGCAGCAGAGTCCATGCCTTTTCTCCTGGAATGTGCAAGAAGTCGTGGTCC
AGAGTATCTTTCACAGATGTGGAAGTTCATATGTGATCCCTTAATCAAAGCTATTGGGACCGAACCTGATACAGATGTAC
TTTCAGAAATAATGAATTCGTTTGCAAAATCCATTGAGGTCATGGGAGATGGTTGCCTTAATGATGAACACTTGGAAGAA
CTGGGAGGAATACTGAAAGCAAAACTTGAAGGACACTTTAAAAACCAAGAATTACGACAGGTTAAAAGACAAGAAGAAAA
CTATGATCAACAGGTTGAGATGTCTCTGCAAGATGAAGATGAGTGTGATGTTTACATTCTGACCAAAGTATCAGATATTT
TGCATTCATTATTTAGTACTTACAAGGAAAAGATTTTACCATGGTTTGAACAGCTACTTCCATTAATTGTAAATCTTATT
TGTTCAAATAGGCCATGGCCAGACAGACAGTGGGGATTGTGCATATTTGATGATATCATAGAGCACTGCAGTCCAACTTC
ATTTAAATATGTGGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGACAACAACCCTGAAGTTAGGCAGGCTGCTG
CTTATGGCTTGGGTGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCTTTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTTATTGCTACAGAGAATTGCATCTCAGCAATAGGGAAAAT
TTTGAAGTTTAAGCCTAACTGTGTAAATGTAGACGAAGTTCTTCCACATTGGTTATCATGGCTTCCACTGCATGAAGACA
AAGAGGAAGCTATTCAGACTTTGAATTTTCTCTGTGACTTAATTGAAAGTAACCATCCAATTGTAATTGGCCCAAATAAT
TCCAATCTTCCCAAAATAATCAGTATAATTGCAGAAGGAAAAATTAATGAGACTATTAACTATGAAGATCCTTGTGCCAA
ACGCCTAGCTAATGTTGTTCGTCAGGTACAGAGTTCTGAAGAATTGTGGTTGGAATGCATATCCCACCTTGATGATGAAC
AGCAGGAAGCTCTGCAGGAGTTGATAAATTTTGCT

ORF - retro_cpor_57 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.65 %
Parental protein coverage: 63.8 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPTLPSDVQTAIKSELLMIIQME
E.YENIPG..K.TFLL.A.RN.....E.RQMAA.LLRRLLSS.F.EVYP.LP.DVQ...K.EL......E
RetrocopyEIYENIPGLCKTTFLLDAVRNRRVGYEVRQMAAALLRRLLSSGFEEVYPNLPFDVQRDVKIELILAVKLE
ParentalTQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGLREAALHIFWNFPGIFGNQQQHYL
T..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DS..S.N..L.E.ALH.FW.FPGIFGNQ..H.L
RetrocopyTHTSMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSIYSKNVVLWEVALHVFWHFPGIFGNQDRHDL
ParentalDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFKHFADLLPGFLQAVNDSCYQNDDSVLKSL
D.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.ALFK.FADLLPG.LQAVNDSCYQ.DDSVL.SL
RetrocopyDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIALFKDFADLLPGILQAVNDSCYQDDDSVLESL
ParentalVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEVIVTLSETAAAMLRKHTNIVAQTIPQMLA
VEIADTVPKYL.P..E.TLQLSLKLCGD..L.N.QRQLALEVIVTLSETA..ML.KHTNI.AQ..P..LA
RetrocopyVEIADTVPKYLGPYIEDTLQLSLKLCGDSRLSNLQRQLALEVIVTLSETATPMLKKHTNIIAQAVPHILA
ParentalMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
MMV.L..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGLGGK.VLPM.KEHIMQMLQ.PDWK.RHAGLM
RetrocopyMMVELQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGLGGKIVLPMTKEHIMQMLQSPDWKCRHAGLM
ParentalALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTM
ALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC...GQMATDFAP.FQKKFHE.VIAALL.TM
RetrocopyALSAIGEGCHQQMEPILDETVNSVLLFLQDPHPRVRAAACTTLGQMATDFAPSFQKKFHETVIAALLRTM
ParentalEDQGNQRVQAHAAAALINFTEDCPKTLLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVA
E.QGNQRVQ.HAA.ALI.F.EDCPK.LL..YLD..VK.LHSI.V.KLQELI..GTKL.LEQ.VT.IASVA
RetrocopyENQGNQRVQSHAASALIIFIEDCPKSLLVLYLDGMVKNLHSILVIKLQELIRNGTKLALEQLVTTIASVA
ParentalDTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTD
DT.EEKFVPYYD.FMPSL.HIVE.AVQK.L..LRGKTIECIS..GLAVGKEKFMQD.S.VM.LLLK.Q.D
RetrocopyDTMEEKFVPYYDTFMPSLRHIVELAVQKDLKTLRGKTIECISHVGLAVGKEKFMQDISNVMELLLKAQSD
ParentalFNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDDDGWEFV
....EDDDPQ.SYM.SAWARMCKILGK.FQQYLP.V..PL.KTAS.KP.VALLDTQD.ENMSDDDGW.FV
RetrocopyLSNIEDDDPQTSYMVSAWARMCKILGKDFQQYLPLVIEPLIKTASAKPDVALLDTQDVENMSDDDGWQFV
ParentalNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPLLKFYFHDDI
NLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQVVKLM.PLLKFYFHD..
RetrocopyNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYTEQVVKLMIPLLKFYFHDNV

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 37 .50 RPM 91 .68 RPM
SRP017611_kidney 20 .94 RPM 81 .45 RPM
SRP017611_liver 10 .62 RPM 61 .68 RPM
SRP040447_lung 15 .06 RPM 107 .82 RPM
SRP040447_skeletal_muscle 13 .60 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_57 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_57 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,


Copyright © RetrogeneDB 2014-2017