RetrogeneDB ID:

retro_sita_35

Retrocopy
location
Organism:Foxtail millet (Setaria italica)
Coordinates:1:42039017..42041501(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:Si016314m.g
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Si021242m.g
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_sita_35
ATGATGGCTGATGCTCCGGCGGTGCATGATTCCGGCGGCGACAGCGAGCTTGAGGACCAATCCTACCAGCAGGAGCCTGC
CTTCGAGGCTTTCATGTGCCCTCTCACCAAACAGGTGATGCAGGACCCCGTGACCATCGAGACGGGGCAGACCTTCGAGC
GGGAGGCCATCCACAAGTGGTTCCGGGAGTGCAGGGACAGCGGGAGGACGCCCACCTGCCCCCTCACCCAGGCGGAACTT
CGCACCACCGACATGACCCCCAGCATAGCCCTGCGCAACGTCATCGACGAGTGGAGGGCCAGGAACCAGGACAAGGAGCT
CGACAAGGCCTGCGCCTCCCTCACCCAGCTCGACATGCCCTCCGAGGACGACGCCCTGCGTGCCCTCCTCTACATCTCCC
AGGTGTGCCACAGGAGCGGCGCTAACAAGAACCTGGTGCGCAGGCAGGGCATCATACCGGCCATCGCCGCCATGCTCAAG
AGCAGCAGCAGGAGGGTTCGCCTCAAGTCTCTCGAGGTACTCCGCGTCGTCGTCGAGGACAACGACGACAACAAGGAAGA
GCTCGGCAAAGGCGACACCATCCGCACCATCATCAAGTTCTTGTCCAACGACCATTTCCAGGAGAGGGAGCTGGCGGTGT
CGCTGCTGTACGAGCTCTCCAAGCTCGACCCCATATGCCAAAGGATCGGTGCGGTCTACGGGGCAATACTTCTCTTGGTC
GGGATGGGGAGCAGCAAATCGGAGAACCTCGTGGCCGTGGAGAAAGCCGAGAACACGCTCAAGAACCTGGAGAAGCACGA
GACGAACGTCAAGCAGATGGCCGAGAACGGCAGGCTGCAGCCTCTGCTTACCAAGCTCATCGAAGGCACACCTCAGGTTC
AGGTGGCCATGGCGGAGTACCTTGGCGAGCTTGCACTGGCCAACGACGTCAAGGTTGTGGTGGCGGAGCAGGTCGGGGAG
CTGCTGGTGAGCATCATGAAGACGGGCAGCCTGCCGGCGAGGGAGGCCACGCTCAAAGCCCTCAGGGAGATATCGTCCAA
CGAGTCCAGCGCCAGGATCCTGCTGCAGGCGGGCATCCTGCCGCCGCTGGTGAAGGACCTCCTCTCCGTGGGCGCCGGCC
ACCTGCCCATGCGGCTCAAGGAGGTGTCGGCCGCCATCCTGGCCAACCTGGTGGCATCGGGCGCCGGCTTCCGGTCCATC
CTGGTGGACGACGAGAGCGGGGAAACGCTGGTGTCGGAGGACGTGGTGCACAGCCTGCTCCACCTCATCAGCAACACCGG
GCCCGCCATCGAGTGCAAGCTCCTCAGCGTCCTCGTCGGCCTCACTGGGTCCGCGGCAACGGTGGCCGACGTGGTCTCCG
CCATCCGCAGCTCCGGCGCCACCATCAGCCTGATCCAGTTCGTGGAGGCGGCGCACCGGGAGATCCGCCTCGAGTCCCTC
AAGTTGCTGCGCAACGTGTCGCCGTACATGGGCGCGGAGCTGGCGGACGCCATCGGAGGCCACCTGGGCAGCCTGGTGAG
GGCGGTCTCCGACGAGCGCGGCGGCGTGACGGAGGAGCAGGCGACGGCGGCGGGGCTGCTGGGCGACCTCCCCGAGCGGG
ACTGGAACCTGACGCGGCAGCTGCAGGACCTGGGCGCGTTCCGGGCGCTGGCGTCGAGGCTGGCGGAGCTCCGGCGGGGC
ACCATCCGCGGCAGCAACCGGCACCTGGCGCCCTTCACGGAGGGCGCCGTCAAGGTGCTCTACAGGGTCACGTGCGCGCT
GGGGGAGGCGGAGGAGGAGGACCTGTACGTGGAGGTGGCGCGGGAGTTGGGCCTGGCGCCGCTCTTCGTAGAGCTGCTGC
AGCAGATGAGCAGCGCCGTGCTGCTCTACTCCGCCATGGCGCTGGAGAACCTGTCGCTGCAGTCGGGGAGGTTAACGGCC
GTGCCGGAGCCGCCGGCGCCGCGGGGCGGCCTCCTCATGTGCGCGTGCTTCGGGAAGCAGCCCCCGCCGGCGCCGCCCGG
CGCTCTGGGGACGTGCCGCGTGCACGGCGGCTTCTGCTCGCTGCGGGAGAGCTTCTGCCTGGCGGAGGGCGGGTGCAAGG
CGGTGGAGCGGCTGGTGGCGTGCCTGGAGCACGCCGACGCGCCGGTGGTGGAGGCAGCGCTGGTGGCGCTGTCGACCCTG
CTGGGGGACGGCGTGGCGAACACGGCGGAGGGCGTGCTGGTGCTCGGTGAGGCGGAGGGCCTGCGCCCCGTCGTCGAGCT
GCTGGTGGAGAACCGGACGGAGGCGCTGCAGCGCCGGGCGGTGTGGGCAGTGGAGCGCATCCTCCGCGTCCAGGACATCG
CCGAGGAGGTGGCGGCGGACCAGACCGTTGCGTCGGCGCTAGTGGAGGCCTACCGCAACGGCGACGCCCGCACCCGCCAC
ACGGCGGAGCGCGCGCTCCGACACCTGGACAGGATCCCAAACTTCTCCACCGCCTTCCACCAAGCCAAAGCCAGGGGGGC
ATGA

ORF - retro_sita_35 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.28 %
Parental protein coverage: 78.64 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVQDGHYDSTSQSTDSLRVEPIYESFLCPLTKQVMRDPVTIDSGVTFERDAILKWFNDCLHSGKRLICPVT
V.D...DS......S...EP..E.F.CPLTKQVM.DPVTI..G.TFER.AI.KWF..C..SG....CP.T
RetrocopyVHDSGGDSELED-QSYQQEPAFEAFMCPLTKQVMQDPVTIETGQTFEREAIHKWFRECRDSGRTPTCPLT
ParentalKKELSTTDLNPSIALRNTIDEWMNRNEAAKLDVARKSLTSDCTES--DILQALQYVDEICQRSRSSRQVV
..EL.TTD..PSIALRN.IDEW..RN....LD.A..SLT.....S..D.L.AL.Y....C.RS......V
RetrocopyQAELRTTDMTPSIALRNVIDEWRARNQDKELDKACASLTQLDMPSEDDALRALLYISQVCHRSGANKNLV
ParentalRRDGLISMIADLLKNSSTKVRQKALETLRSISKDDNDNKVEIAAGDNIRTIVKFLNHGQTQEKEKAVSLL
RR.G.I..IA..LK.SS..VR.K.LE.LR....D..DNK.E...GD.IRTI.KFL.....QE.E.AVSLL
RetrocopyRRQGIIPAIAAMLKSSSRRVRLKSLEVLRVVVEDNDDNKEELGKGDTIRTIIKFLSNDHFQERELAVSLL
ParentalYELSENKDLSERIGSVSGAILILVGLSSSKVENSLIVDRAEKTLENLESCEKNVRQMAENGRLQPLLRLL
YELS.......RIG.V.GAIL.LVG..SSK.EN...V..AE.TL.NLE..E.NV.QMAENGRLQPLL..L
RetrocopyYELSKLDPICQRIGAVYGAILLLVGMGSSKSENLVAVEKAENTLKNLEKHETNVKQMAENGRLQPLLTKL
ParentalLEGSPDMQLSMAAYLGELVLSNDVKVLVAQTAGSTLVNIMKNGNREAREAALKALNQISSYDASAKILIE
.EG.P..Q..MA.YLGEL.L.NDVKV.VA...G..LV.IMK.G...AREA.LKAL..ISS...SA.IL..
RetrocopyIEGTPQVQVAMAEYLGELALANDVKVVVAEQVGELLVSIMKTGSLPAREATLKALREISSNESSARILLQ
ParentalAGILPPLITDLFTVGSNQLPMRLKEVSANILANVVASGARFESIPL-DHSRQTLVSEDIVHNLLHLISNT
AGILPPL..DL..VG...LPMRLKEVSA.ILAN.VASGA.F.SI...D.S..TLVSED.VH.LLHLISNT
RetrocopyAGILPPLVKDLLSVGAGHLPMRLKEVSAAILANLVASGAGFRSILVDDESGETLVSEDVVHSLLHLISNT
ParentalGPAIECKLLQVLVGLTDSSTSVQSIVDAIKSSGAIVSLIQFVEAPQREVRMNSIKLLNNISPYMGQELAD
GPAIECKLL.VLVGLT.S...V...V.AI.SSGA..SLIQFVEA..RE.R..S.KLL.N.SPYMG.ELAD
RetrocopyGPAIECKLLSVLVGLTGSAATVADVVSAIRSSGATISLIQFVEAAHREIRLESLKLLRNVSPYMGAELAD
ParentalAFRGNFSQLSSLVRVIAD-NNGISEEQAAAAGLVADLPMRDSVLTRRLHQDGAFATINLKVLRIRQGEIR
A..G....L.SLVR...D...G..EEQA.AAGL..DLP.RD..LTR.L...GAF..........R.G.IR
RetrocopyAIGGH---LGSLVRAVSDERGGVTEEQATAAGLLGDLPERDWNLTRQLQDLGAFRALASRLAELRRGTIR
ParentalG-GRFVNPFLEGLVRIVSRITYVL---DDDPDFIAVAREYNLTALFTDLLQMNGLDTVQIVSATALEKLS
G..R...PF.EG.V....R.T..L...........VARE..L..LF..LLQ......V...SA.ALE.LS
RetrocopyGSNRHLAPFTEGAVKVLYRVTCALGEAEEEDLYVEVARELGLAPLFVELLQQMS-SAVLLYSAMALENLS
ParentalHQSKHLTKILPAPNP
.QS..LT.....P.P
RetrocopyLQSGRLTAVPEPPAP

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_35 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 Si021242m.g 1 retrocopy
retro_sita_35 ,




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