RetrogeneDB ID:

retro_sbic_40

Retrocopy
location
Organism:Sorghum (Sorghum bicolor)
Coordinates:5:7018612..7020765(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:Sb05g005320
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Sb06g004530
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sbic_40
ATGTGGCTTTTCTGGCGCACCAGGAACCGCTTCTCCCTCGAGGAGCTCCGGTACCTAACAGATCAGCTGCAAAAGGTTCA
TGCCGTCAACGAAGCTAATCAGGATGTCGTGATTGAAGCACTGAGATCGATTGCCGAGCTTATGATATACGGCGACCAGC
ACGATCCATCGCTTTTTGAGTATTTCATGGAGAAACAGATCGTGGGTGAATTCGCTCGTATCCAAAGGATCTCTGATCTG
TCAAGAGTGTCACTCCAGTTGCTGCAGACAATGGGCATCATGATCCAAAATCTCAGACATGAACATTCAGTTCATTACAT
TTTGAGCAGTGAGCACATCAACTTCTTCGTCACGCACCCATTCGATTTCCGGATCGATGAGTTGTTGTCCTACTACATAT
CTTTTCTCCGGGCGATAAGTGGGAAGCTGAACAAGGATACAATTTCTTTGCTGGTGAAGACGGAAGACGATGAGGTCACT
TCCTTTCCTCTCTATGTCGAGGCCTTGAAGTTTGCTTTTCACCAGGATAGCATGATTCGAGTTGCTGTACGTACCTTGAC
GCTCAATGTCTACCACATTGGAGATGAATCTGTTAACAGATTTGTTTCCCGTGTGCCTGTATCAGATTATTTTTCAGACA
TGGTCCAGCATTTTCAGAAGCAGTGCATTGACTTGGATAAGCTGGTTGCACACTCCTCGCAAACTGCAGATTTTTCTCTG
CCAATGTCTTGTGTTGAAGATGCGATTGTGCAGATTGAAGACACACTGTATTATTTCAGTGATGTTATGTCTTCTGGTAT
TCCAGATCTTGAAAGGTTCATCACTGACAATTTCTTGCAAGCTGTGGTGTTTCGGTTATTACTACCGTCATTGCTGAGGC
AGAGCATAGATTTGGACCTAAGTGTCACTACATCCATGTATCTGCTTTGCTGTATACTGCACATTTTGAAGAATAAGGAT
ATGGCAAGTACTGTAGCTGCTGCACTTTTTCATCAACCTGATTGCCCTGATGAAACGAAGCAAGGGACACCTCCTGATGG
GTATACATCTGAGCATGATAATTGCAGGTCTGAGAATCATTGCAACACTGCCTCTGCTGTCGAGCAATCAAATGAGGATG
AGCCAAATTCTCTGTCTTCTGTTAGTTGGGAACGCTTGCCCAACCATTCGCTGCCAAGTGATTGCTGCCAAGGCAACACG
CCAAGGGAACACTTGCTGTCCTATATCACAGAAGGAGATGATTCACAAGCTTTGGGTTCATTGTGCTTATTCGCTACATT
ACTGCAGACGAAAGAACTTGACGAATCAATGCTGGATGCACTTGGAATCCTACCTCATAGAAAGCAGCATAAGAAGCTTC
TATTACAAGCTTTAGTAGGTGAAGACCTTGCTGAAGGACAATTATTTTCGTCAAGCAGCGGTCTAATTGATGACAACATT
CACAGTGATTTTGATATTTACGTGAGGAAGCTTCAGGATAAATATGGTCTACAGTGTCATCATCCACGGGCACGGCAAAT
GACTTCCGAAGCTCACAGATATCAGGTGCTCGATGCTTTGGTCGACCTTTTCTGCAGATCGAAGGTTTCTGCAGATGTTC
GCTTGGTTTGTGGTTGGCTTTTCCGGCAACTGCTGCCCCAAGGAGAGGAAGAATTCACTGCTTTTCATCTAAGACGACTA
AAGGATTCACACAAGGATTGTATCTCAAAGCTTTCGGAGGAATCTGGAGGATGCTGGTGTGACATGCTTCTTCCTATCAT
TAAAGACGCTTGGAGGAACTGCAAGAAAGAAATTGAGGCATCTTCAGTTGCCATCGCAGAGGGAGTCTATGCGATGGTTA
AGCATAGCATTCTTGCTAGTTGTAGGAAAGATGATGAAGACTGCCAAGAGGAAAGCCTGCCCAATAAATACTTAGAATAT
CTTTCATGCATCTCCAAGGACATAGAAACATTTTGCTGGTGCAAGCAACCAATGGGGAAAGTAGACATCGATACTAGCAG
AATGGAGGAATACTCACACAGCTATACTGAACCGCTGATGTTGACTGGTGACACGAAGAGAGGTTGTACAAGGGATACTT
TCAGCAGCTATAAGCTGCAAGTGCTTACCGTGCTCAAAACAATTGCTATAAACTGCAACAGCTTAACATGCTG

ORF - retro_sbic_40 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.54 %
Parental protein coverage: 67.08 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMWLFWRTRNRFSLEELRYLTDQLQKVHVVNEANKDFVIEALRSIAELMIYGDQHDPSFFEYFMEKQIMGE
MWLFWRTRNRFSLEELRYLTDQLQKVH.VNEAN.D.VIEALRSIAELMIYGDQHDPS.FEYFMEKQI.GE
RetrocopyMWLFWRTRNRFSLEELRYLTDQLQKVHAVNEANQDVVIEALRSIAELMIYGDQHDPSLFEYFMEKQIVGE
ParentalFARVLRISKLSRVSLQLLQTMGIMIQNLRNEHSIYYIFSNEHINFLITFPFDFRIDEMLSYYISFLRAIS
FAR..RIS.LSRVSLQLLQTMGIMIQNLR.EHS..YI.S.EHINF..T.PFDFRIDE.LSYYISFLRAIS
RetrocopyFARIQRISDLSRVSLQLLQTMGIMIQNLRHEHSVHYILSSEHINFFVTHPFDFRIDELLSYYISFLRAIS
ParentalGKLNKNTISLLVKTKNDEVTSFPLYVEALKFAFHEDSMIRVAIRTLTLNVYHVGDESVNRFVSRVPLSDY
GKLNK.TISLLVKT..DEVTSFPLYVEALKFAFH.DSMIRVA.RTLTLNVYH.GDESVNRFVSRVP.SDY
RetrocopyGKLNKDTISLLVKTEDDEVTSFPLYVEALKFAFHQDSMIRVAVRTLTLNVYHIGDESVNRFVSRVPVSDY
ParentalFSDIVQHFQKQCIDLDKLVAHSSRNANSSLPMPSVEDAIVQIEDTLYYFSDVMSSGIPDLERFITENILQ
FSD.VQHFQKQCIDLDKLVAHSS..A..SLPM..VEDAIVQIEDTLYYFSDVMSSGIPDLERFIT.N.LQ
RetrocopyFSDMVQHFQKQCIDLDKLVAHSSQTADFSLPMSCVEDAIVQIEDTLYYFSDVMSSGIPDLERFITDNFLQ
ParentalVLVFRFLFPSLQRQSTDLDLSVTTSMYLLCCILHIFKNKDMASTVAAALFHQPDGLYDKEQGT-PNGFTS
..VFR.L.PSL.RQS.DLDLSVTTSMYLLCCILHI.KNKDMASTVAAALFHQPD......QGT.P.G.TS
RetrocopyAVVFRLLLPSLLRQSIDLDLSVTTSMYLLCCILHILKNKDMASTVAAALFHQPDCPDETKQGTPPDGYTS
ParentalEHDNCKFENYCTTSSAVEQSNEDEPNSLSSVSWKRLPNNSPPSDCCQGNTPREHLLSYITEGDDSQALGS
EHDNC..EN.C.T.SAVEQSNEDEPNSLSSVSW.RLPN.S.PSDCCQGNTPREHLLSYITEGDDSQALGS
RetrocopyEHDNCRSENHCNTASAVEQSNEDEPNSLSSVSWERLPNHSLPSDCCQGNTPREHLLSYITEGDDSQALGS
ParentalLCLFATLLQTKELDESMLDALGILPQRKQHKKLLLQALVGEDHAERQLFSSSSSLTDDSICSDFDIYVRK
LCLFATLLQTKELDESMLDALGILP.RKQHKKLLLQALVGED.AE.QLFSSSS.L.DD.I.SDFDIYVRK
RetrocopyLCLFATLLQTKELDESMLDALGILPHRKQHKKLLLQALVGEDLAEGQLFSSSSGLIDDNIHSDFDIYVRK
ParentalLQDKYGLQCHHP--RQMTSKAHRYQVLDAIVNLFCRSKVSADVRLVGGWLFRQLLPHGEEEFTAFHLRRL
LQDKYGLQCHHP..RQMTS.AHRYQVLDA.V.LFCRSKVSADVRLV.GWLFRQLLP.GEEEFTAFHLRRL
RetrocopyLQDKYGLQCHHPRARQMTSEAHRYQVLDALVDLFCRSKVSADVRLVCGWLFRQLLPQGEEEFTAFHLRRL
ParentalKDSHKDCSSKLSEESGGCWCDMLLPIVKEAWRNCKKAIEASS
KDSHKDC.SKLSEESGGCWCDMLLPI.K.AWRNCKK.IEASS
RetrocopyKDSHKDCISKLSEESGGCWCDMLLPIIKDAWRNCKKEIEASS

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






RNA-Seq - click to see more details

Sorghum bicolor was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sorghum bicolor was not studied using ChIP-Seq data.

EST - click to see more details

Sorghum bicolor was not studied using EST data.

TSS - click to see more details

Sorghum bicolor was not studied using FANTOM5 data.

Lab - click to see more details

retro_sbic_40 was not experimentally validated.

Retrocopy orthology:
Sorghum bicolor 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
Sorghum bicolor Sb06g004530 1 retrocopy
retro_sbic_40 ,




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