RetrogeneDB ID:

retro_sita_47

Retrocopy
location
Organism:Foxtail millet (Setaria italica)
Coordinates:3:48588879..48590532(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Si024562m.g
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sita_47
ATGGCATCCCGGTTTTTCTTTCTTGTCGTTGCCGTCGTGGCCCGGCTCTGCAGCGCCGCTATGGCGACTGGTGGTCAGGC
CGACGACATCTTGCGGCCGTGGCCGCCTGACTGCTCGACGGCGGACAACTACACGGCCGACAGCCAGTACAAGAAGAACC
TGGACCAGCTCCTCGCCGCGCTCCCCGCGGCGGCCGGCGACAACGGCTGGTTCTACGAGGGCAGCGCCGGGGCCGGCACC
GACGACGAGGTGTTCGGCCTCATCATGTGCTACGCCGACCACAACGCGACGGCGTGCCTCGACTGCCTCTCCAGGGCGCC
CGCCGGGATCGCCACGGTGTGCCCGGGCAGCCGGAACGTTCGCGCCATGTACGACGCGTGCGTGCTCCGGTACTCGGCGG
CGCCGATCCCGGCCACCGCGGACCTCAGCTACTTGCACTCCGTGAACGGGACCGTCCGTGGGGTGCCCGTCGGCGTCACC
TCGGAGAGCGCCCGGGCAGCCTGGGTGGCGCTGATGAGCGAGCTCACGGGCGGCGTCGCTGGCTCGCCGCTGCGGCTCGC
CAACGGCAGCACGCCGTACTCGGGCTCGCAGGCTATGTACGGCCTGGCGCAGTGCACCAGGGACCTCAACGCCAGCGAGT
GCTCCAGCTGTGTCTCAAGCTACACGGACAGGCTGGGGGACCTGTTCCCCAACAACACCGGCGGCGCCATCAAGGGGTAC
AGCTGCTACCTGCGCTACCAGGTGGGCGTCCTCGACATCACCCTGCCGCCGGCGCCAACTCCCCCGGCGATATCCGTAGG
ACCTTCATCGTCTTCCAAGAGCGCCGATCATTCCAAGACCATCGGGATCCTGATCGGCGTGTTCGTCGGTTCCAGCTTGA
TAGCCCTGGTCTTCTTCATGCGACTCCCCCGGCGAAAGAGGGAAAAAAGTAAGCTCGTCGATGAAGAAGCAGCAAGAGAG
ATGGACGACGAGTTCGAGGAAGGGACCGGGCCAAAGCAGTTCCGCTACAGCGAGCTCGCCATGGCCACCGACTACTTCTC
GGACAAGCGCAAGCTCGGAGAAGGTGGGTTCGGGTCAGTGTACAGAGGCTACATTAAGGAGATGGACCTTCACGTCGCCA
TCAAGAGGGTGTCCAAGGGTTCGAAGCAGGGCAGGAAGGAGTACGCCTCGGAGGTCAGGATCATCAGCCTGCTGCGGCAC
CGTAACCTTGTGCAGCTCATCGGTTGGTGCCATGGCGGCGGCGAGCTCCTCCTCGTGTACGAGCTGATGCCCAACGGCAG
CCTCGACACGCACCTCTACAGCGCCAGGGACGGCGCCCTGCTGCCATGGCCGCTGCGGCACGAGATCGTGCTCGGCCTGG
GGTCGGCCCTGCTGTACCTTCATCAGGATTGGGAGCAGTGCGTTCTTCACAGGGACATCAAGCCGAGCAACGTGATGCTG
GACGCGTCCTTCCACGCCAAGCTCGGCGACTTCGGGCTCGCCAGGCTCGTCGGCCACGGCCGCCGCTCGCACACCACGGT
GATCGCCGGCACCTTGGGCTACATAGACCCCGACTGCATGATCACCGGCAGGGCCAGCACCGAGACTGACGTCTACAGCT
TCGGCGTCGTCCTCCTCGAGATCGCCTGCGGCCGGCGGCCTCTGGTGGCCGTT

ORF - retro_sita_47 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.84 %
Parental protein coverage: 85.51 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPPRLAVALATFALLCAAA---AGQDDKILRPWPPDCSTADNYTADSQYKKNLDQLLAALPAAAGDNGW
MA........A..A.LC.AA....GQ.D.ILRPWPPDCSTADNYTADSQYKKNLDQLLAALPAAAGDNGW
RetrocopyMASRFFFLVVAVVARLCSAAMATGGQADDILRPWPPDCSTADNYTADSQYKKNLDQLLAALPAAAGDNGW
ParentalFYEGSVGTGAD-RVYGLIMCYADYNATACMDCLSRAPAGITTVCPGSRSVRAMYDACTLRYSAAPIPATA
FYEGS.G.G.D..V.GLIMCYAD.NATAC.DCLSRAPAGI.TVCPGSR.VRAMYDAC.LRYSAAPIPATA
RetrocopyFYEGSAGAGTDDEVFGLIMCYADHNATACLDCLSRAPAGIATVCPGSRNVRAMYDACVLRYSAAPIPATA
ParentalDLAVLYIVYLTFP--EVAVTSEGVRAAWVPLMSELTGGAAASPLRLASGSTPYSSSQSSQEMYGLAQCSR
DL..L..V..T.....V.VTSE..RAAWV.LMSELTGG.A.SPLRLA.GSTPYS.SQ....MYGLAQC.R
RetrocopyDLSYLHSVNGTVRGVPVGVTSESARAAWVALMSELTGGVAGSPLRLANGSTPYSGSQA---MYGLAQCTR
ParentalDLNASECSRCVSSYVGQLGKLFPNNSGGVIKGYSCYLRYQVAALDITLPPAPAPAT----PPPAGGPSSS
DLNASECS.CVSSY...LG.LFPNN.GG.IKGYSCYLRYQV..LDITLPPAP.P......P.........
RetrocopyDLNASECSSCVSSYTDRLGDLFPNNTGGAIKGYSCYLRYQVGVLDITLPPAPTPPAISVGPSSSSKSADH
ParentalSKT-GIVVGVSVGSVSILILLGFSMWLLLRRRRRKEANLHEETRAMEDEFEKGSGPKRFRYGELAVATDN
SKT.GI..GV.VGS...LI.L.F.M.L..R.R........E..R.M.DEFE.G.GPK.FRY.ELA.ATD.
RetrocopySKTIGILIGVFVGSS--LIALVFFMRLPRRKREKSKLVDEEAAREMDDEFEEGTGPKQFRYSELAMATDY
ParentalFSDKYKLGEGGFGSVYRGFLKEMNLHVAIKRVSKGSNQGRKEYASEVRIISRLRHRNLVQLIGWCHGGGD
FSDK.KLGEGGFGSVYRG..KEM.LHVAIKRVSKGS.QGRKEYASEVRIIS.LRHRNLVQLIGWCHGGG.
RetrocopyFSDKRKLGEGGFGSVYRGYIKEMDLHVAIKRVSKGSKQGRKEYASEVRIISLLRHRNLVQLIGWCHGGGE
ParentalLLLVYELMPNGSLDKYLHSADN--KLSWPLRHKIVLEIASAILYLHQEWEQCVLHRDIKPSNVMLDASFT
LLLVYELMPNGSLD..L.SA.....L.WPLRH.IVL...SA.LYLHQ.WEQCVLHRDIKPSNVMLDASF.
RetrocopyLLLVYELMPNGSLDTHLYSARDGALLPWPLRHEIVLGLGSALLYLHQDWEQCVLHRDIKPSNVMLDASFH
ParentalAKLGDFGLARLVDHARGSHTTVAAGTLGYMDPERRARGRASARSDVYSFGVVLLEVACGRSPAVVL
AKLGDFGLARLV.H.R.SHTTV.AGTLGY.DP.....GRAS...DVYSFGVVLLE.ACGR.P.V..
RetrocopyAKLGDFGLARLVGHGRRSHTTVIAGTLGYIDPDCMITGRASTETDVYSFGVVLLEIACGRRPLVAV

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_47 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 Si024562m.g 1 retrocopy
retro_sita_47 ,




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