RetrogeneDB ID:

retro_sita_30

Retrocopy
location
Organism:Foxtail millet (Setaria italica)
Coordinates:9:402227..403784(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Si035206m.g
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Si026237m.g
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sita_30
ATGGCGGGCAAGATCAAGACGGTGGTGGTGCTCGTGCAGGAGAACCGCTCCTTCGACCACATGCTGGGGTGGATGAAGAA
GTCCATCAACACCGACATCGACGGCGTCACCGGCGACGAGACCAACCACGTCGACGCCTCCGACCCCTCCTCCCGCGCCG
TCCGCTTCAGCGACCGCTCTCAGTACGTGGACCCCGACCCGGGCCACTCCATCCAGGCCATCTACGAGCAGGTCTACGGC
GTCGCCTTCGCCGACGCCGCCGCCACCCCCATCACCCCGCCCGGCGTGCCTGCGCCGCCCATGAGCGGCTTCGTGCAGCA
GGCGGAGAAGGAGAAGCCCGGCATGGCGGACACCGTCATGAGCGGCTTCCTCCCCGACGCCGTCCCCGTGTACCGCGAGC
TGGTGCGCGAGTTCGCCGTGTGCGACCGGTGGTTCGCGTCCGTGCCGGCGTCGACGCAGCCCAACCGGCTGTTCGTGCAC
TCGGCTACCTCCCACGGCCTCGTCAGCAACGACACCAAGCAGCTCGTCTGGGGCCTGCCGCAGAGGACAATCTTCGACAA
CCTCCATGACCAGGGCTTCTCCTTCGGCATCTACTACCAGTACCCGCCGTCGACGCTCTTCTACCGGAACCTGCGCCAGC
TCAAGTACGCCGGCAACTTCCACCCGTTCGACCTCGACTTCCGGCGCCATTGCCGGGAGGGCAAGCTGCCCAACTACGTC
GTCGTCGAGCAGCGCTACTTCGACCTCAAGATCCTCCCCGGCAACGACGACCACCCCTCCCACGACGTCGCCGAGGGCCA
GCGCTTCGTCAAGGAGGTCTACGAGGCGCTGCGCTCCGGCCCCCAGTGGGGGGAGGCGCTCCTCGTCATCACCTACGACG
AGCACGGCGGCTTCTACGACCACGTCCCCACACCCGCAGCCGGCGTGCCCAGCCCCGACGGCATCGCCAGCGCGCCGCCC
TTCTGCTTCCAGTTCGACCGACTCGGCGTCCGCGTCCCGGCGCTCCTCGTCTCGCCGTGGATCGAGCCGGGAACCGTGCT
GCACGGGCCGCCGTCGGGGCCGTACCCGACCTCGGAGTTCGAGCACTCCTCCATCCCGGCCACCGTCAAGAAGATCTTCA
ACCTCGACGGCTTCCTCACCAGGCGCGACGCATGGGCGGGAACCTTCGACTCCGTGCTCACCCGCGACACGCCGCGCACC
GACTGTCCAGTCACCCTGCCTGAGCCGGTGAAGCTGCGGCGGGCGGCGGCGGTGGAGCATGCGCCGCTGTCGGAGTTCCA
GGAGGAGCTGGTCCAGCTCGCCGCGGTGCTCAACGGCGACCACACCAAGGACTCGTACCCGAACAAGCTCGCCGACAGCA
TGACGGTGGCGGAGGCGGCCAGGTACTGCGTCGACGCCTTCAGGGCCTTCTTGGACGAGTGCGACCGCTGCAACAAGTGC
GGCGAGGACGGGTCCCACATCCCCACGGTGACGCCGTCGTCTTCGCCGGAGAAGAACAAGAGCAGCTTCGCGTCCAAGGT
GCTGGCGTGCCTTGCGTGTGGCCATTCCTCTTCCTAA

ORF - retro_sita_30 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.12 %
Parental protein coverage: 99.8 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAGKIKTVVVLVQENRSFDHMLGWMK-SLNPEIDGVTGAELNHAVAGDATSPAVHFGNASQYVDPDPGHS
MAGKIKTVVVLVQENRSFDHMLGWMK.S.N..IDGVTG.E.NH..A.D..S.AV.F...SQYVDPDPGHS
RetrocopyMAGKIKTVVVLVQENRSFDHMLGWMKKSINTDIDGVTGDETNHVDASDPSSRAVRFSDRSQYVDPDPGHS
ParentalFMAIYEQVYGDPYTWGSGAPATKAGVAAPPMSGFAQQAEKERPGMSATVMNGFRPDAVPVYRELVREFAV
..AIYEQVYG.........P.T..GV.APPMSGF.QQAEKE.PGM..TVM.GF.PDAVPVYRELVREFAV
RetrocopyIQAIYEQVYGVAFADAAATPITPPGVPAPPMSGFVQQAEKEKPGMADTVMSGFLPDAVPVYRELVREFAV
ParentalCDRWFASVPTSTQPNRMFVHSATSHGLVGNDKKLLRAGMPQRTIFDALHDAGHSFGIYYQFPPAVLFYRN
CDRWFASVP.STQPNR.FVHSATSHGLV.ND.K.L..G.PQRTIFD.LHD.G.SFGIYYQ.PP..LFYRN
RetrocopyCDRWFASVPASTQPNRLFVHSATSHGLVSNDTKQLVWGLPQRTIFDNLHDQGFSFGIYYQYPPSTLFYRN
ParentalMRQLKYMSKFHPYDLDFKRHCKEGKLPNYVVIEQRYLDLKLFPGNDDHPSHDVAHGQRLVKEVYEALRSS
.RQLKY...FHP.DLDF.RHC.EGKLPNYVV.EQRY.DLK..PGNDDHPSHDVA.GQR.VKEVYEALRS.
RetrocopyLRQLKYAGNFHPFDLDFRRHCREGKLPNYVVVEQRYFDLKILPGNDDHPSHDVAEGQRFVKEVYEALRSG
ParentalPQWHETLLVITYDEHGGFFDHVPTPTEGVPSPDGIVSAPPIGFAFDRLGVRVPAMFISPWIEPSTVIH-R
PQW.E.LLVITYDEHGGF.DHVPTP..GVPSPDGI.SAPP..F.FDRLGVRVPA...SPWIEP.TV.H..
RetrocopyPQWGEALLVITYDEHGGFYDHVPTPAAGVPSPDGIASAPPFCFQFDRLGVRVPALLVSPWIEPGTVLHGP
ParentalPSGPEPTSQYEHSSIPATVKKIFNLKEFLTKRDAWAGTFESVLTRATPRTDCPEKLPEPVRLRSVEAEEH
PSGP.PTS..EHSSIPATVKKIFNL..FLT.RDAWAGTF.SVLTR.TPRTDCP..LPEPV.LR...A.EH
RetrocopyPSGPYPTSEFEHSSIPATVKKIFNLDGFLTRRDAWAGTFDSVLTRDTPRTDCPVTLPEPVKLRRAAAVEH
ParentalREISEFQSELVQLGAALNGDHAREAYDTGELVEGMTVAEAADYCHGAFARFREECRRCHECGMDGSHVPT
...SEFQ.ELVQL.A.LNGDH....Y....L...MTVAEAA.YC..AF..F..EC.RC..CG.DGSH.PT
RetrocopyAPLSEFQEELVQLAAVLNGDHTKDSY-PNKLADSMTVAEAARYCVDAFRAFLDECDRCNKCGEDGSHIPT
ParentalVQPEAAVAPSASKQLCSCLPCFS
V.P........S......L.C..
RetrocopyVTPSSSPEKNKSSFASKVLACLA

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_30 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 Si026237m.g 1 retrocopy
retro_sita_30 ,




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