RetrogeneDB ID:

retro_tcac_15

Retrocopy
location
Organism:Cacao (Theobroma cacao)
Coordinates:8:4233470..4236662(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:TCM_034672
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:TCM_046769
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_tcac_15
ATGGCTTCTTCGATCGAGAACAAGAACATTGTTGAAGATTCCGAAGACAAAGCTCTCGACGTGTCGGGGAAAGCCGTAGA
ATTCTCTTTCTTCGGCAACCCTGAAGAGAAGGTCGGTTCCTCTGTCGAGGGGCTTTATTTGTACAATAATGATTTTAATT
TGATTCCCGAGGCAGTTTCCCAGTTTGGGAAATTGAAATTTTTGAAATTCTTCGGTAACGAGATTAATCTGTTACCATCC
GTGGTTGGGAATTTGGCAAAATTAGAGTCCTTGAAGATGAAGATTTCTTCGCCGGGGTTAAACGGCGTCTCGTTTCGCGA
ACTCAGCGAGTTGAAGGAGCTCGAGCTCAGTAGAACCCCTCCTCAGCCTTCGAGGTTAACTGCATTGACTGAGATCGCTG
GAATCAAGGGCTTGACTAGGCTCACTTTGTGTTACTTCTCTATCAGGTACCTTCCATCAGAGATTGGATGCTTAACGAAT
TTGGAATTTTTCGATATTTCTTTTAATAATATCAAGAACTTGCCTGCTGAAATTAGTAATTTGAATGAGTTAATCACTTT
GAAAGTTGTTCATAATAAGCTAATGGAGCTGCCTTCGAGTTTGTCTAAGTTGAATAAGTTGGAGAACTTGGATTTGTCCA
ATAATAGATTAACTTCTTTGAGGCCGCTAGAATTAGAGGCAATGCATAGGCTTAAGAATTTGAATGTTGGGTACAATAAA
ATTATGAATTGTTGTCAAATCCATATTCCCGGATGGATAAGCTGTGATTTGGAAGGGAATAAAAGTAATGGCAAAGGTTT
ATCTGTTGGTGTATGTGAGAGTGTTGAAGAGAAAGAAGTGAGTGTTTCTAGTGACTGCCCTCGAGGCAATACCTCATTGG
AGATGTTGAGTCAATCTGGGAAAAGTAGATTCGAATCCCAGAGTTTGAGTTCGGGTAAGCGATGGAAGCGAAGACAACAA
GACAAGTTAAGAAATTACAAGAAGTTGAAAAGTGAAGGGAATGGTGAAGATGTTCTTAGCTCTGAGACTGGTTTGCAAAG
TGAGTTGTATGTGGTAGATCTGAACGGTGATGAGAATGATAAGGGTGAGAGTGAAAATTCATTTATTGGAGAAAATGCAG
TGGTGGAAACTTTAGCCTCCGAAGAAAATTGCATTTGCCTGGATCATGAAGCCATAAAAGAGGGCAAAAAGGAGTATGAT
GAGCAAGATGAAATTTCTGTTTCCAGCCAGGGGAAAGGTTCATATTCAGAATCGTTCAACAGTAGTTGCATGTCAAAGAG
GCATTCCAGTTGTGATCTTGATGATAATCCCAAGACATGCAAGTATCAGAAGCCAAATGATGGTAATTTTTCATTATCAC
GCAAGTATAACAATACTTCATTTTGTAGCGTTAAAGACCGGATCCCAGATGGCTTTTATGATGCGGGACGTGACCGGCTT
TTCATGTCACTTGAGAGTTATGAGCGTATTCTGCATCTCGATTCACGTGAAGTCATTCTTGCTGACAGGGAGAAGGATGA
ACAGTTAGATGCAATTACTCTTTCTGCTCAAGCTTTGATATCCAGTTGGAAGAAATTAAATGGCTTAGCCAGTAACGGGG
AACCAACTCCAATGGATAACCTTCAAATTGCATCATTGCTTGCATTGTTTGTATCGAATCGTTTTGGAGGCAGTGATAGA
AGTTTTTCCATTGAAAAGACTCGAAAAGCAGTGTCTGGTTCAAACTATCTGAAGCCATTTGTTTGCAGCTGTGCTACTGG
AAATAATGATTGTGTAAATGATTCTACCGAATGGAATTTTGGTACTATACAAGATATCAGCATTGCTGATCTTTGTGATA
AATCACTATGTTCTACCAAGTCAAGACTGAATTCTGTTGTAGTTCCTATAGGAACTATGCAGTTTGGTGTGTGTAGACAC
AGAGCATTGCTCATGAAGTATTTGTGTGATCGTATGGTACCACCAGTGCCTTGTGAGCTGGTCAGGGGATACCTTGACTT
CTATCCACATGCTTGGAATGTAGTACTTGTCAAAAAAGGTGATTTATTGGTCCGCATGGTAGTTGACGCATGCCATCCTG
ATGACATAAGAGAAGAGATGGATCCAGAATATTTTTGCCGATACATTCCCTTGACTCGGACCAAAGATTTTCTCTCAAAT
GAATGCAATCTTGACCCTGATTGTTTTCCTTCCTTGTCCACAAGTGAAAAAATTGAAAAGACACCAAATGTGTCCCTCAT
TAAGTGCTCATTTGGTTCAGTTGAGGCAGCAGCAAAGGTGCGTACAGTAAATGTCCTCGGAACTTCAATGAATGAGATTA
GAAACTTTGAGTATAGTTGTTTAGGAGAGATAAGAATGTTAGGAGCTTTGAAACACTCCTGCATTGTAGAATTGTATGGG
CACCAAATATCTTCGAAGTGGGTTCCCTCAGCGGCTGAAAGGCCCGAGCATCGCATAATACAGTCTGCCATTTTAATGGA
GTATGTAAAAGGTGGATCTTTGAAGTGCCAAATAGAGAAGTTATTGAAAGCTGGCAAGAAACATTTCCCATTGGATTTTG
CGTTGTGTGTTGCTCACGATGTTGCTTGTGCATTGGCAGCACTACATTCTAAACACATTATTCATCGGGATATAAAAAGC
CACAATATTTTGATTGATTTGGATGAGAAGAGGGCTGATGGAACACCTATTGTCAAGCTTTGTGATTTTGATAGAGCAGT
GCCTCTTCGTTCTTTCTTGCATAAATGCTGTATAGCTCATACAGGAATACATCCTCCTAATGTTTGTGTTGGAACTCCAC
GTTGGATGGCTCCAGAAGTTTTAAGGACAATGCAGAAACCTAATTTATATGGACTGGAAGTGGATATTTGGTCATATGGA
TGCTTGATTTATGAATTATTAACTCTGCAAATTCCATACTTCGATTTTTCTGATGATCAAATGCATGACTTTATTCAAAT
GGGCAAACGACCTCCACTAACTGATGAACTGGAGGCATTACTATTGCTGGATGAGTTTGCAATATCTCAAGAGTTGGACA
GACCAAAATCTGAAATCGAATCACTTAGATTCCTTATTAATGTGTTCCATCGTTGTACTGTAGAAAATCCTACTGATCGT
CCAAAGGCTGAAGAACTCTATGAAATGTTTCATGCACATGCAAGTAACTTGAGAAGTTTTGAAGAGGTTTAG

ORF - retro_tcac_15 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.28 %
Parental protein coverage: 56.94 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQDEGSSSDICKSNSKSKRHSDRDLN-NPKPCKSRKPTDYCYNLSRKYSTNSFCGTEDHLPDGFYDAGRDR
Q..GS.S....S...SKRHS..DL..NPK.CK..KP.D....LSRKY...SFC...D..PDGFYDAGRDR
RetrocopyQGKGSYSESFNSSCMSKRHSSCDLDDNPKTCKYQKPNDGNFSLSRKYNNTSFCSVKDRIPDGFYDAGRDR
ParentalPFMPLSRYEQTFHLDSREVILVDRERDEELDAIALSAQALVFHLKNLNGLAKDRERVPVDNLQIASLLAL
.FM.L..YE...HLDSREVIL.DRE.DE.LDAI.LSAQAL....K.LNGLA...E..P.DNLQIASLLAL
RetrocopyLFMSLESYERILHLDSREVILADREKDEQLDAITLSAQALISSWKKLNGLASNGEPTPMDNLQIASLLAL
ParentalFVSDHFGGSDRSGIVERTRKALSGSNYKKPFICTCSTGNGDSVSASNK-TLDTVEDIVFSELCERSLRSI
FVS..FGGSDRS...E.TRKA.SGSNY.KPF.C.C.TGN.D.V..S......T..DI....LC..SL.S.
RetrocopyFVSNRFGGSDRSFSIEKTRKAVSGSNYLKPFVCSCATGNNDCVNDSTEWNFGTIQDISIADLCDKSLCST
ParentalKSRRNSIVVPIGTLQFGVCRHRALLMKYLCDRMEPPVPCELVRGYLDFMPHAWNIILVRRGDSWVRMVVD
KSR.NS.VVPIGT.QFGVCRHRALLMKYLCDRM.PPVPCELVRGYLDF.PHAWN..LV..GD..VRMVVD
RetrocopyKSRLNSVVVPIGTMQFGVCRHRALLMKYLCDRMVPPVPCELVRGYLDFYPHAWNVVLVKKGDLLVRMVVD
ParentalACHPHDIREETDPEYFSRYIPLSRKKASLRTESTPVFSCSFPSMTISDEIERVASSSLIRCKYGSMEAAA
ACHP.DIREE.DPEYF.RYIPL.R.K..L..E......C.FPS...S..IE.....SLI.C..GS.EAAA
RetrocopyACHPDDIREEMDPEYFCRYIPLTRTKDFLSNECNLDPDC-FPSLSTSEKIEKTPNVSLIKCSFGSVEAAA
ParentalKVRTLEVLGASLDEVKNFEYSCLGEVRILGALKHPCIVEMYGHQISSKWIPIGDGKSEHRILQSAILMEY
KVRT..VLG.S..E..NFEYSCLGE.R.LGALKH.CIVE.YGHQISSKW.P......EHRI.QSAILMEY
RetrocopyKVRTVNVLGTSMNEIRNFEYSCLGEIRMLGALKHSCIVELYGHQISSKWVPSAAERPEHRIIQSAILMEY
ParentalIKGGSLKTHIEKLAEAGEKHVPVDFALCIARDIASALVELHSKHVIHRDIKSENILIDLDEKRVDGSPIV
.KGGSLK..IEKL..AG.KH.P.DFALC.A.D.A.AL..LHSKH.IHRDIKS.NILIDLDEKR.DG.PIV
RetrocopyVKGGSLKCQIEKLLKAGKKHFPLDFALCVAHDVACALAALHSKHIIHRDIKSHNILIDLDEKRADGTPIV
ParentalKLCDFDRAVPLRSFLHTCCIAHVGIHPPNVCVGTPRWMAPEVLRAMHKRNQYGLEVDIWSFGCLLYELLT
KLCDFDRAVPLRSFLH.CCIAH.GIHPPNVCVGTPRWMAPEVLR.M.K.N.YGLEVDIWS.GCL.YELLT
RetrocopyKLCDFDRAVPLRSFLHKCCIAHTGIHPPNVCVGTPRWMAPEVLRTMQKPNLYGLEVDIWSYGCLIYELLT
ParentalLQVPYSGLSELHIHELLQMGKRPRLTEELEALDSLSESAMTQSGTELDGKEAEVDTLRFLVDVFCRCTEE
LQ.PY...S....H...QMGKRP.LT.ELEAL..L.E.A..Q...ELD....E...LRFL..VF.RCT.E
RetrocopyLQIPYFDFSDDQMHDFIQMGKRPPLTDELEALLLLDEFAISQ---ELDRPKSEIESLRFLINVFHRCTVE
ParentalNPTDRPTAKELYDILLEHTNGFRN
NPTDRP.A.ELY.....H....R.
RetrocopyNPTDRPKAEELYEMFHAHASNLRS

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






RNA-Seq - click to see more details

Theobroma cacao was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Theobroma cacao was not studied using ChIP-Seq data.

EST - click to see more details

Theobroma cacao was not studied using EST data.

TSS - click to see more details

Theobroma cacao was not studied using FANTOM5 data.

Lab - click to see more details

retro_tcac_15 was not experimentally validated.

Retrocopy orthology:
Theobroma cacao 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
Theobroma cacao TCM_046769 1 retrocopy
retro_tcac_15 ,


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