RetrogeneDB ID:

retro_sita_3

Retrocopy
location
Organism:Foxtail millet (Setaria italica)
Coordinates:9:5156387..5157761(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Si040038m.g
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Si035607m.g
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sita_3
ATGGCGGCAACTCGCGTCCTGGTGCTGCCTTACCCCGCGCAGGGCCATGTCATCCCTATGATGGAGCTCTCCCACAGCCT
CGTCGAGCACGGTGTCAAGGGCACCTTCGTCAACACCGAGCTGAACCACGGCCTCATCCTTGGCGCCTTGGCGAGCAGGG
ACAGCGTGCTCGGCGGTGTCGACATGGTGTCGGTGCCCGACGGCCTGGGCTGCGGCGAAGACCGGAAGGACCTCGCCCGT
CTCACCGACTCGTTCTCGAAGGTCATGCCCGTCGAGCTGGGGAAGCTCGTTGCCAGGATCAATGCTGATGCGCGGGGGCG
CGGGAGGATCACCTGGTTGGTCGCCGACGTGAACATGGCGTGGGCCTTTCCCGTGGCGAAGAGGCTCGGCCTCCGGGCCG
CCGGGTTCTGCCCGTCGTCGGCGGCGATGTTCGCGACAAGGATCAGAATTCCGGAGATGATCAGCGATGGCATCCTTGAC
GACAGGGGCTGGCCGAGGCGGCGCGGCACGTTCCAGCTGGCTCCGGCGATGCCACCCATCGACACGTCGGAGTTCTCGTG
GAACCGCGCCGGCGACACCAGGGGCCAGCCGGTCATCTTCCAGTTGATCCTCCGGAACAACGCGGCCACGCACCTCGCCG
AGGCCATCGTGTGCAACACCATCCAGGAGCTGGAGCCCGGAGCCCTCGCGCTGTTCCCCAGCGTCCTTCCCGTGGGCCCG
CTCTCCTCCGACAAGCCGGTGGGAAGCTTCTGGACCGAGGACGCCTCCTGCGCGGCGTGGCTGGACGCGCAGCCGGCCAA
CTCCGTCGTGTACGTGGCGTTCGGCAGCTTCGCCGCCTACGACACCGCGCAGCTCGTGGAGCTGGCCGAAGGGCTCGCGC
TGACCTCCCGGCCTTTCCTGTGGGTGGTCAGGCCGGGGTCGGCGGGCGAGGAGCTCCTCGACCGGCTCCGCCGCCGCGCC
GCGCCGCGCGGGCGCGTGGTGAGCTGGTGCCCGCAGCGGCGCGTGCTGGCGCACCCCGCGGTCGCCTGCTTCCTGACGCA
CTGCGGCTGGAACTCGACGATGGAGGCCGTGGCCAACGGCGTGCCGCTCCTGTGCTGGCCATACTTCACCGACCAGTTCC
TGAACCAGAGCTACATCTGCGACGTGTGGAGGACGGGGATCAAGGTGCCGCGGCCGGCCGGCGGCGGGACGACGACGGGG
CTCGTGGGAAGGGACGTGGTGCGGGGGAAGGTGGAGGAGCTGCTCGGCGACGCGGGGACGAAGGCGAGGGCGCTCGCGCT
ACGGGACCTCGCCCGGCGGGCCGTCGGCGAGGACGGGTCGTCGCGCCGGAATCTCGAACGATTCGTGGACCTCGTGAAAG
GATCTGCGACCTGA

ORF - retro_sita_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.56 %
Parental protein coverage: 95.85 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAPHVLALPFPAQGHIIPLMQLSHRLVEHGIEVTFVNTEANHTLVLDAMAANGAGCPSLDGIRLVGVPD
MAA..VL.LP.PAQGH.IP.M.LSH.LVEHG...TFVNTE.NH.L.L.A.A........L.G...V.VPD
RetrocopyMAATRVLVLPYPAQGHVIPMMELSHSLVEHGVKGTFVNTELNHGLILGALASRDS---VLGGVDMVSVPD
ParentalGLADGDDRKDLGKLVDALSQHMPCYLEELVGRI--EASGGTKISWLVADEGMGWAFEVAKKLGIRAACFW
GL..G.DRKDL..L.D..S..MP..L..LV.RI...A.G...I.WLVAD..M.WAF.VAK.LG.RAA.F.
RetrocopyGLGCGEDRKDLARLTDSFSKVMPVELGKLVARINADARGRGRITWLVADVNMAWAFPVAKRLGLRAAGFC
ParentalTGSAAFLASMLRIPQLIQDGVIDEKGWPKRQETFQFAPGMPPLHTSHLSWNNAGAPKDQPAIFQLVVRNN
..SAA..A...RIP..I.DG..D..GWP.R..TFQ.AP.MPP..TS..SWN.AG....QP.IFQL..RNN
RetrocopyPSSAAMFATRIRIPEMISDGILDDRGWPRRRGTFQLAPAMPPIDTSEFSWNRAGDTRGQPVIFQLILRNN
ParentalEAKDLAEVTVCNSFGDAEPAAFKLYPDILPVGPLFADVQFKKPVGQFLPEDARCLEWLDAWPDRSVVYVA
.A..LAE..VCN.....EP.A..L.P..LPVGPL..D....KPVG.F..EDA.C..WLDA.P..SVVYVA
RetrocopyAATHLAEAIVCNTIQELEPGALALFPSVLPVGPLSSD----KPVGSFWTEDASCAAWLDAQPANSVVYVA
ParentalFGSFTVFNPHQFEELALGLELTGRPFLWVVRPDFVAGLSKPWLDEFQRRVGDSGLIVSWCPQQQVLAHRA
FGSF......Q..ELA.GL.LT.RPFLWVVRP..........LD...RR....G..VSWCPQ..VLAH.A
RetrocopyFGSFAAYDTAQLVELAEGLALTSRPFLWVVRP---GSAGEELLDRLRRRAAPRGRVVSWCPQRRVLAHPA
ParentalVACFVSHCGWNSTMEGVRNGVPFLCWPYFTDQFQNESYICNVWRTGLAVVRGADGVVTKEELSGKVERVI
VACF..HCGWNSTME.V.NGVP.LCWPYFTDQF.N.SYIC.VWRTG..V.R.A.G..T.......V.R..
RetrocopyVACFLTHCGWNSTMEAVANGVPLLCWPYFTDQFLNQSYICDVWRTGIKVPRPAGGGTTTGLVGRDVVRGK
ParentalGDEGIRERVGALRDAARRSIA
..E.........R..A.R..A
RetrocopyVEELLGDAGTKARALALRDLA

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_3 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 Si035607m.g 1 retrocopy
retro_sita_3 ,


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