RetrogeneDB ID:

retro_sbic_19

Retrocopy
location
Organism:Sorghum (Sorghum bicolor)
Coordinates:3:63017916..63019735(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Sb03g034880
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Sb10g005550
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sbic_19
ATGAACCAGGATAATTATTTTGAAGAGGCCCTCAAAATGCGTAACCTGTTAGAGCAGTACAACTATTATCACGGGAGCAG
AAAACCAACACTTCTGGGAGTTCGGGAACATGTTTTCACTGGATCAGTCTCTTCACTTGCTTGGTTCATGTCTGCACAGG
AGACAAGCTTTGTTACCCTTGGTCAGCGTGTCCTAGCTAATCCATTGAAAGTACGGATGCATTATGGGCATCCTGATGTA
TTTGACCGCCTTTGGTTTTTAACTCGGGGTGGTATAAGTAAGGCATCAAGAGTGATCAATATCAGCGAGGACATCTTTGC
TGGTTTCAACTGTACCTTACGTGGTGGCAATGTTAGTCACCATGAATATATTCAGGTTGGTAAGGGCCGTGATGTTGGCC
TCAATCAGATATCAATGTTTGAAGCAAAGGTTTCCAGTGGCAACGGTGAGCAGACCCTTAGTAGGGATGTATACAGGCTT
GGTCATAGACTGGATTTCTTTCGGATGCTCTCTGTGTTTTATACAACAGTGGGGTTCTACTTCAACACAATGCTGGTGGT
CTTGACAGTTTACACATTTGTTTGGGGACGCCTGTATCTAGCTCTCAGTGGTCTTGAGGCTGGTATTCAGGGCAGTGCTA
ATTCAACCAACAACAAAGCCTTGGGTACTGTGCTTAATCAGCAGTTCATCATACAGCTTGGCTTCTTCACTGCCTTGCCA
ATGATTATAGAAAACTCTCTTGAACAAGGTTTCCTACCTGCTATCTGGGATTTTTTCACAATGCAAATGAATTTTTCATC
TGTGTTCTACACATTTTCCATGGGAACTAAGAGCCATTACTATGGCCGGACAATCCTTCATGGTGGTGCAAAATACCGTG
CTACTGGTCGTGGTTTTGTTGTGCAGCACAAGAGTTTTGCTGAAAATTACAGGCTGTATGCTAGGAGCCACTTCATAAAG
GCAATAGAACTTGGAATAATATTGACTGTGTATGCTGCACACAGTGTTATTGCCAAGAATACACTTGTTTACATAATCAT
GAATATATCTAGCTGGTTTCTGGTGGTATCATGGATTATGGCTCCATTTGCTTTTAATCCATCTGGTTTTGATTGGTTGA
AAACAGTGTACGATTTTGATGATTTCATGAACTGGATATGGTATCCCGGTGGTCTCTTTTCTAAGCCTGAGCAGAGCTGG
GAAGTGTGGTGGTTTGAGGAGCAAGATCATCTACGGACCACTGGTCTTTGGGGAAAGATTTTGGAAATACTGTTAGATCT
CAGGTACTTCTTTTTCCAGTATGGGGTTGTGTACCAGCTGAAGATAGCCAACAATAGCAGAAGTATTGCTGTCTATCTGC
TTTCCTGGATATGTGTGGCTGTGATTTTTGGTGTGTTCGTCCTAATGTCCTATGCTCGAGACAAGTATGCCGCAAAGGAG
CACCTTTACTACCGGGTTGTCCAAACTGTTGTCATCGTTCTTGCAGTGCTGGTGCTGATATTGTTTCTGAAGTTCACGGA
ATTTGAAATCATTGACATCTTCACTAGTCTTTTGGCATTTATTCCTACTGGTTGGGGCTTGATTTCGATCGCTCAAGTAA
TTCGGCCATTCATCGAATCCACTGTGGTGTGGAACAGTATTATTTCTGTGGCTCGCTTGTATGAGATACTGCTTGGAGCA
TTCATTATGGCACCAGTTGCATTGCTGTCCTGGTTGCCGGGATTTCAAGAAATGCAGACAAGGGTACTTTTCAATGAAGG
TTTCAGCAGGGGCCTCCAGATATCCCGTATTCTTACTGGAAAAAAGACAAATACAGTTT

ORF - retro_sbic_19 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.63 %
Parental protein coverage: 55.18 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNQDNYLEEALKMRNLLEEFNENHGVRQPTILGVREHIFTGGVSSLAWFMSNQETSFVTIGQRVLANPLK
MNQDNY.EEALKMRNLLE..N..HG.R.PT.LGVREH.FTG.VSSLAWFMS.QETSFVT.GQRVLANPLK
RetrocopyMNQDNYFEEALKMRNLLEQYNYYHGSRKPTLLGVREHVFTGSVSSLAWFMSAQETSFVTLGQRVLANPLK
ParentalVRFHYGHPDVFDRIFHITRGGISKASCGINLSEDIFAGFNSTLRRGNVTHHEYIQVGKGRDVGLNQISLF
VR.HYGHPDVFDR....TRGGISKAS..IN.SEDIFAGFN.TLR.GNV.HHEYIQVGKGRDVGLNQIS.F
RetrocopyVRMHYGHPDVFDRLWFLTRGGISKASRVINISEDIFAGFNCTLRGGNVSHHEYIQVGKGRDVGLNQISMF
ParentalEAKVACGNGEQILSRDIYRLGHRFDFFRMLSCYFTTVGFYISSMMVVIIVYVFLYGRLYLALSGLEFAIM
EAKV..GNGEQ.LSRD.YRLGHR.DFFRMLS...TTVGFY...M.VV..VY.F..GRLYLALSGLE..I.
RetrocopyEAKVSSGNGEQTLSRDVYRLGHRLDFFRMLSVFYTTVGFYFNTMLVVLTVYTFVWGRLYLALSGLEAGIQ
ParentalKQARMRGNRALQAAMGSQSIVQLGLLMALPMFMEIGLERGFRSALGDFIIMQLQLCSVFFTFSLGTKSHY
..A....N.AL......Q.I.QLG...ALPM..E..LE.GF..A..DF..MQ....SVF.TFS.GTKSHY
RetrocopyGSANSTNNKALGTVLNQQFIIQLGFFTALPMIIENSLEQGFLPAIWDFFTMQMNFSSVFYTFSMGTKSHY
ParentalFGRTILHGGAKYRATGRGFVVRHVRFAENYRMYSRSHFVKALELMLLLVVYELYGDVATDSTAYILLTSS
.GRTILHGGAKYRATGRGFVV.H..FAENYR.Y.RSHF.KA.EL...L.VY......A.....YI....S
RetrocopyYGRTILHGGAKYRATGRGFVVQHKSFAENYRLYARSHFIKAIELGIILTVYAAHSVIAKNTLVYIIMNIS
ParentalMWFLVITWLFAPFLFNPSGFEWQKIVDDWDDWTKWISSRGGIGVPANKAWESWWEEEQEHLQSTGLLGRF
.WFLV..W..APF.FNPSGF.W.K.V.D.DD...WI...GG........WE.WW.EEQ.HL..TGL.G..
RetrocopySWFLVVSWIMAPFAFNPSGFDWLKTVYDFDDFMNWIWYPGGLFSKPEQSWEVWWFEEQDHLRTTGLWGKI
ParentalWEIILSLRFFIFQYGIMYHLNISAGNKSISVYGLSWLVIVAVVMVLKVVSMGRKKFSADFQLMFRLLKLF
.EI.L.LR.F.FQYG..Y.L.I.....SI.VY.LSW........V....S..R.K..A...L..R.....
RetrocopyLEILLDLRYFFFQYGVVYQLKIANNSRSIAVYLLSWICVAVIFGVFVLMSYARDKYAAKEHLYYRVVQTV
ParentalLFIGSVGTLAVLFTVLHLTVGDIFASFLAFAPTGWAILQISQASKPVIKACGLWGSVKALSRGYEYLMGI
.....V..L............DIF.S.LAF.PTGW....I.Q...P.I.....W.S.....R.YE.L.G.
RetrocopyVIVLAVLVLILFLKFTEFEIIDIFTSLLAFIPTGWGLISIAQVIRPFIESTVVWNSIISVARLYEILLGA
ParentalVIFVPVAVLAWFPFVSEFQTRLLFNQAFSRGLQISRILAGGK
.I..PVA.L.W.P...E.QTR.LFN..FSRGLQISRIL.G.K
RetrocopyFIMAPVALLSWLPGFQEMQTRVLFNEGFSRGLQISRILTGKK

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_19 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 Sb10g005550 1 retrocopy
retro_sbic_19 ,


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