RetrogeneDB ID:

retro_sita_7

Retrocopy
location
Organism:Foxtail millet (Setaria italica)
Coordinates:3:50375740..50377174(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Si021926m.g
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Si021994m.g
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sita_7
ATGGAAAGGAAGCCCGCCGCTGCGGCGGCGCTGGTAGTAGTAGTAGTAGTAGTACTCGCCGCCGCGCTCTTCTCCGTCGG
CGAGGCGGCGCACCCTCGTCGCTGTGTGACGAGCACGTACCGGCGGAAGCACCAGGCCTCCGACGACATGCCGATGGACG
CGGACGTGTTCGCGGTGCCGCCGGGCCGCAACGCGCCGCAACAGGTGCACATCACGCTCGGGGACCAGACCGGCACGGCC
ATGCTCGTGTCCTGGGTCACCGTGGAGGCCGAGGGCAACAGCACCGTCCTGTACGGCCGCGCCGCGGACAGGCTCGACCT
CGCCGCCGAGGGCACCACCACCCGCTACACCTTCTACAACTACACCTCCGGCTTCATCCACCACTGCACGCTCACCGGCC
TGGACCACGGCACCCGGTACTACTACGCCATGGGGTTCGGCGACACGGTGCGCACCTTCTGGTTCACCACGCCGCCCCCG
CCCGGCCCTGGCGCGCCGCTCCGGCTGGGTCTCATCGGCGACCTCGGCCAGACGCCCGACTCCAACAGCACGCTCACCCA
CTACGAGCAGCACCCCGGCGACGCCGTGCTCTTCGTCGGCGACCTCTCCTACGCCGACAAGCACCCGCTCCACGACAACA
ACCGCTGGGACACCTGGGGCCGCTTCTCCGAGCGCAGCGTCGCGTACCAGCCCTGGATCTGGACCGCCGGCAACCACGAG
ATCGACTACGCGCCGGAGATCGGGGAGACGGTCGCGTTCAAGCCCTTCTCCCACCGCTACCCGACGCCGTACCGCGCCAG
CGACTCGTCGGAGCCGTACTGGTACTCGGTGAAGATGGGGCCCGCGCACATCATCGTGCTCTCCTCCTACTCGGCCTTCG
GCAAGTACACGCCGCAGTGGAAGTGGCTGGAGCAGGAGCTGAAGCGCGTGGACCGGGAGACCACGCCGTGGCTCTTCATC
AGCGCGCACGTGCCCTGGTACAACAGCAACAACTTCCACTTCATGGAGGGCGAGCCGACGCGCGTGCAGTTCGAGCAGAT
GGCCGTCGACGCCCGCGTCGACATCGTCTTCGCCGGCCACGTCCACGCCTACGAGCGCAGCCACCGGTACTCCAACATCA
AGTACAACATCACCGACGGCAAGTGCACGCCCGTCGCCGACCGCCGCGCCCCAGTATACATCGTCATCGGCGACGGCGGC
AACATCGAGGGCCTCGCCGACGAGCTCACCTGGCCGCAGCCGGCCTACTCGGCGTTCCGGGAGTACAGCTACGGCCACGC
CGTGCTGGACATCAAGAACCACACGCACGCACACTACGCCTGGTACCGCAACCACGACGGCAACAAGGTCACCGCGGACA
CCACCTGGTTCACCAACCGCTACCACATGCCCAACCACGACGACTCCGTCTACTCGAACACTGCCTACGTGTAA

ORF - retro_sita_7 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.92 %
Parental protein coverage: 94.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVTSEYRRKLEATVEMPLDADVFRVPPGYNAPQQVHITLGNQEGTAMIVSWVTPSELGSSTVMYGGAPHKL
VTS.YRRK..A...MP.DADVF.VPPG.NAPQQVHITLG.Q.GTAM.VSWVT....G.STV.YG.A...L
RetrocopyVTSTYRRKHQASDDMPMDADVFAVPPGRNAPQQVHITLGDQTGTAMLVSWVTVEAEGNSTVLYGRAADRL
ParentalELRAEGTHTRYDYFNYTSGFIHHCTLKNLKHSSKYYYAMGFGHTVRTFWFTTPPKPGPDAPYKFGLIGDL
.L.AEGT.TRY...NYTSGFIHHCTL..L.H...YYYAMGFG.TVRTFWFTTPP.PGP.AP...GLIGDL
RetrocopyDLAAEGTTTRYTFYNYTSGFIHHCTLTGLDHGTRYYYAMGFGDTVRTFWFTTPPPPGPGAPLRLGLIGDL
ParentalGQTFDSNRTLSHYESNGGDAVLFVGDLSYADNHPLHDNNRWDTWARFVERSVAYQPWIWTAGNHELDFAP
GQT.DSN.TL.HYE...GDAVLFVGDLSYAD.HPLHDNNRWDTW.RF.ERSVAYQPWIWTAGNHE.D.AP
RetrocopyGQTPDSNSTLTHYEQHPGDAVLFVGDLSYADKHPLHDNNRWDTWGRFSERSVAYQPWIWTAGNHEIDYAP
ParentalELGETTPFKPFSHRYPTPYRAAGSTEPFWYSVKIASAHVIVLASYSAYGKYTPQWTWLQDELKRVDRKTT
E.GET..FKPFSHRYPTPYRA..S.EP.WYSVK...AH.IVL.SYSA.GKYTPQW.WL..ELKRVDR.TT
RetrocopyEIGETVAFKPFSHRYPTPYRASDSSEPYWYSVKMGPAHIIVLSSYSAFGKYTPQWKWLEQELKRVDRETT
ParentalPWLLVLMHSPWYNSNGYHYMEGETMRVQFEQWLVDAKADLVLAGHVHAYERSHRVSNVAYDIVNGKSTPV
PWL....H.PWYNSN..H.MEGE..RVQFEQ..VDA..D.V.AGHVHAYERSHR.SN..Y.I..GK.TPV
RetrocopyPWLFISAHVPWYNSNNFHFMEGEPTRVQFEQMAVDARVDIVFAGHVHAYERSHRYSNIKYNITDGKCTPV
ParentalRDQGAPVYVTIGDGGNIEGIADNFTRPQPSYSAFREASFGHATLEIKNRTHAYYAWHRNQDGAKVVADGL
.D..APVY..IGDGGNIEG.AD..T.PQP.YSAFRE.S.GHA.L.IKN.THA.YAW.RN.DG.KV.AD..
RetrocopyADRRAPVYIVIGDGGNIEGLADELTWPQPAYSAFREYSYGHAVLDIKNHTHAHYAWYRNHDGNKVTADTT
ParentalWLTNRYWMPTDD
W.TNRY.MP..D
RetrocopyWFTNRYHMPNHD

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_7 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 Si021994m.g 1 retrocopy
retro_sita_7 ,




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