RetrogeneDB ID:

retro_sita_17

Retrocopy
location
Organism:Foxtail millet (Setaria italica)
Coordinates:4:35880797..35882423(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:Si007876m.g
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Si007904m.g
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sita_17
ATGGAGCTGGCGGCAGCGGCCTCGCCGGCGCTTGAAGCTCCCTTGCCCTCCTCCTCGACTGTCCTCCAAGTGTTACTGCT
CATGGTGATGCTCGTGTACCTCGTCCAAACCCTCATGGCGCGGCGGAAGAGCACGTGCACCGCGCCGCTCCCGCCAGGGC
CGACGCCATGGCCCGTTGTCGGCAACCTGCCGGAGATGCTGCTCAGCGACAAACCGGCGTTCAGGTGGATCCACCTCATT
ATGATCAAAATGGGCACCGACATCGCCTGCGTCAAGCTAGGCGGCGTCCACGTGATCCCGATCACCTGCCCCATGATCGC
ACGCGAGGTGCTCAAGAAGCAGGACGCCAACTTCGCCTGCCGGCCGCTGAGCTTGGCCTCCAAGACATTCAGCAGAGGCT
ACATGGACGCCGTGATGTCCCCCTACGGCGACCAGTGGAGGAAGATGCGCCGCGTGCTAGCCTCCGAGGTCGTTTGTCCT
TCCCGCCACAGGTGGCTCCACGACAAGCGCGCCGCCGAGGCCGATAACCTCACCCGCTTCGTCTACAACCTCGCCGGCGG
AGCGGGGTCCGGCGGCGCCGCCGTCGACGTCAGGCACGTCGCGCGCCACTATTGTGGGAACGTCGTCCGCCGCCTCGTCT
TCAATAGGCGCTACTTCGGCGAGCCGCGGCCCGACGGCGGCCAAGGCCCGCTGGAGGTGCAGCACGTGGATGCGGTGTTC
ACCTCCCTGGGGCTCCTCTACTCCTTCTCCGTCTCCGACTACCTCCCCTGGCTGCTGGGCCTCGACCTCGACGGCCACGA
GAAGATGGTCAGGGAGGCCCAGGAGACGGTGAGCAGGCTGCACGACACGTTCATCAACGAGCGGTGGCGGCAGTGGAAGA
GCGGCGAGAGGCAGGAGCTCGAGGACCTCCTCGACGTGCTCATCACGCTCAAGGATGCCGAGGGCAAACGATCCGTGCTC
ACCGTCGATGAGGTCAGAGCTCAGTTGCAGGACATCACGTTCGCGGCCATGGACAACCCATCGAACGCGGTGGAGTGGGC
GATGGCCGAGATGGTGAACGCTCCGGAGACGATGAGGAAGGCGGTGGCGGAGCTCGATGCCGTCGTCGGCCGGGACCGAC
TGGTGCAGGAGTCCGACATACCGCGGCTCAACTACCTCAAGGCCTGCATCCGCGAAGCGTTCCGCCTGCACCCCGTGGCG
CCGTTCAACGTCCCCCATGTCGCGCTCGCCGACGCCACCGTCGCCGGCTACCACGTCCCCAAGGGCAGCCACGTCATCCT
CAGTCGAATCGGCCTCGGCCGCAATCCTGCCGTCTGGGACGATCCGCTCCGGTTCGACCCTGACCGACACCTCGACGCCA
ATCCCGAGGCGGATGTCACGCTCGCCGAGAACGACCTGCGGTTCATCTCTTTCAGCACCGGTCGCCGCGGCTGCATTGCC
GCTTCACTCGGCACCGCCATGAGTGTCATGCTCTTTGGCAGGCTCTTGCAGGGGTTCGCCTGGAGCAAGCCGGCCGGGAT
GGCGGCCATCGACCTCAGCGAGTCAAGGCACGACATGTTCATGGCCAAGCCGCTGGTGCTGAACGCCGAGCCACGGCTGC
CGGCGAACCTCTACTCGGCTATCTCT

ORF - retro_sita_17 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.44 %
Parental protein coverage: 98.71 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEATAAATSVLGAS-SLTSAILKALLLLVTMVCLVRTIRPQRKTKFTASLPPGPTPWPIVGNLPEMMLN-
ME..AAA...L.A.....S..L..LLL.V..V.LV.T....RK...TA.LPPGPTPWP.VGNLPEM.L..
RetrocopyMELAAAASPALEAPLPSSSTVLQVLLLMVMLVYLVQTLMARRKSTCTAPLPPGPTPWPVVGNLPEMLLSD
ParentalKPAFRWIHHVMKDIGTDIACIKLGGVHVIPITCPAIAREVLRKQDTTFASRPLTFASETFSGGYRNAVLS
KPAFRWIH..M...GTDIAC.KLGGVHVIPITCP.IAREVL.KQD..FA.RPL..AS.TFS.GY..AV.S
RetrocopyKPAFRWIHLIMIKMGTDIACVKLGGVHVIPITCPMIAREVLKKQDANFACRPLSLASKTFSRGYMDAVMS
ParentalPYGDQWRKMRRVLASEIVCPSRHKWLCSKRADEADNITRYVYSLV--KTKSGGAVDVRHVARHYCGNVIR
PYGDQWRKMRRVLASE.VCPSRH.WL..KRA.EADN.TR.VY.L.......G.AVDVRHVARHYCGNV.R
RetrocopyPYGDQWRKMRRVLASEVVCPSRHRWLHDKRAAEADNLTRFVYNLAGGAGSGGAAVDVRHVARHYCGNVVR
ParentalRLVFNRRHFGEPQPDGGPGPLEVQHVDAVFRSLGLLYAFCVSDYLPWLLGLDLDGHEKMVKEANKIVNGL
RLVFNRR.FGEP.PDGG.GPLEVQHVDAVF.SLGLLY.F.VSDYLPWLLGLDLDGHEKMV.EA...V..L
RetrocopyRLVFNRRYFGEPRPDGGQGPLEVQHVDAVFTSLGLLYSFSVSDYLPWLLGLDLDGHEKMVREAQETVSRL
ParentalHDKVIDERWRQWKSGERKEPEDFLDVLITLKAADGK-ALLTIEEVKAQSQDITFAAVDNPSNAVEWALAE
HD..I.ERWRQWKSGER.E.ED.LDVLITLK.A.GK...LT..EV.AQ.QDITFAA.DNPSNAVEWA.AE
RetrocopyHDTFINERWRQWKSGERQELEDLLDVLITLKDAEGKRSVLTVDEVRAQLQDITFAAMDNPSNAVEWAMAE
ParentalTVNNPELLEKAAAELDGVVGRGRLVQESDIPWLCYLKACIREAFRLHPVAPFNVPHVALADATVAGYHVP
.VN.PE...KA.AELD.VVGR.RLVQESDIP.L.YLKACIREAFRLHPVAPFNVPHVALADATVAGYHVP
RetrocopyMVNAPETMRKAVAELDAVVGRDRLVQESDIPRLNYLKACIREAFRLHPVAPFNVPHVALADATVAGYHVP
ParentalKGSHVILSRIGLGRNPAVWDDPLRFDPGRHIIPGDPTAEVTLCENELRFISFSTGRRGCIAASLGTAMSV
KGSHVILSRIGLGRNPAVWDDPLRFDP.RH.....P.A.VTL.EN.LRFISFSTGRRGCIAASLGTAMSV
RetrocopyKGSHVILSRIGLGRNPAVWDDPLRFDPDRH-LDANPEADVTLAENDLRFISFSTGRRGCIAASLGTAMSV
ParentalMLFGRLLQCFTWSKQAAVTTIDLSESRNDTFMAKPLVLHAEPRLPAHLY
MLFGRLLQ.F.WSK.A....IDLSESR.D.FMAKPLVL.AEPRLPA.LY
RetrocopyMLFGRLLQGFAWSKPAGMAAIDLSESRHDMFMAKPLVLNAEPRLPANLY

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






RNA-Seq - click to see more details

Setaria italica was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Setaria italica was not studied using ChIP-Seq data.

EST - click to see more details

Setaria italica was not studied using EST data.

TSS - click to see more details

Setaria italica was not studied using FANTOM5 data.

Lab - click to see more details

retro_sita_17 was not experimentally validated.

Retrocopy orthology:
Setaria italica 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
Setaria italica Si007904m.g 1 retrocopy
retro_sita_17 ,




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