PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Transcription Factor Information
Basic Information? help Back to Top | |||||||||
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TF ID | LOC_Os06g05350.1 | ||||||||
Common Name | LOC4340109, Os06g0145800, OsJ_20114, OSJNBa0007O20.30, OSNPB_060145800, P0036F10.13 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
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Family | Whirly | ||||||||
Protein Properties | Length: 273aa MW: 30161.4 Da PI: 9.73 | ||||||||
Description | Whirly family protein | ||||||||
Gene Model |
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Signature Domain? help Back to Top | |||||||
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No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | Whirly | 192.9 | 4.7e-60 | 97 | 235 | 1 | 139 |
Whirly 1 svyktkaalkvkavrptfealdsgnlklkraGglllelanataerkydWekkqsfalsatevaelvdlaskesceffhdpaakgsneGkvrka 93 s+yk+kaa++++++ p+f+ ldsg+ k+ ++G++ll++a+a+a+r+ydW +kq+f+ls+ e+++l+ l++ +sceffhdp+++ s+eGkvrk+ LOC_Os06g05350.1 97 SIYKGKAAMSLDPRPPQFVPLDSGAYKVVKEGFVLLQFAPAVATRQYDWTRKQVFSLSVWEMGSLLTLGPTDSCEFFHDPFKGRSDEGKVRKV 189 7******************************************************************************************** PP Whirly 94 lkvePlpdGsGlfvnlsvtnslvkgnesfsvPvskaefavlrsllv 139 lkveP pdG f+nlsv+n l++ +e++++P++k+efav+ s ++ LOC_Os06g05350.1 190 LKVEPTPDGNSRFFNLSVQNRLLNIDENIYIPITKGEFAVIVSTFN 235 *****************************************99875 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
Gene3D | G3DSA:2.30.31.10 | 3.1E-79 | 84 | 257 | IPR009044 | ssDNA-binding transcriptional regulator |
SuperFamily | SSF54447 | 6.91E-78 | 89 | 272 | IPR009044 | ssDNA-binding transcriptional regulator |
Pfam | PF08536 | 9.1E-59 | 98 | 232 | IPR013742 | Plant transcription factor |
Gene Ontology ? help Back to Top | ||||||
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GO Term | GO Category | GO Description | ||||
GO:0006281 | Biological Process | DNA repair | ||||
GO:0045893 | Biological Process | positive regulation of transcription, DNA-templated | ||||
GO:0045910 | Biological Process | negative regulation of DNA recombination | ||||
GO:0009508 | Cellular Component | plastid chromosome | ||||
GO:0009570 | Cellular Component | chloroplast stroma | ||||
GO:0003700 | Molecular Function | transcription factor activity, sequence-specific DNA binding | ||||
GO:0003723 | Molecular Function | RNA binding | ||||
GO:0043565 | Molecular Function | sequence-specific DNA binding |
Plant Ontology ? help Back to Top | ||||||
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PO Term | PO Category | PO Description | ||||
PO:0009009 | anatomy | plant embryo | ||||
PO:0001081 | developmental stage | mature plant embryo stage | ||||
PO:0007042 | developmental stage | whole plant fruit formation stage |
Sequence ? help Back to Top |
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Protein Sequence Length: 273 aa Download sequence Send to blast |
MPPPSPPLFL SLPSPPPPPL PHLLPSHRPA AALTLAPALS SRRVSSVCPV ASQRHSDYFD 60 PRAPPPPPPR DGYGGPAYSP PAAQGGQQNG RVFSTYSIYK GKAAMSLDPR PPQFVPLDSG 120 AYKVVKEGFV LLQFAPAVAT RQYDWTRKQV FSLSVWEMGS LLTLGPTDSC EFFHDPFKGR 180 SDEGKVRKVL KVEPTPDGNS RFFNLSVQNR LLNIDENIYI PITKGEFAVI VSTFNYIIPH 240 LMGWSTFTNS IKPEDSRAYT RPQSGPEYEW RR* |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
1l3a_A | 6e-91 | 91 | 270 | 37 | 218 | p24: plant transcriptional regulator PBF-2 |
1l3a_B | 6e-91 | 91 | 270 | 37 | 218 | p24: plant transcriptional regulator PBF-2 |
1l3a_C | 6e-91 | 91 | 270 | 37 | 218 | p24: plant transcriptional regulator PBF-2 |
1l3a_D | 6e-91 | 91 | 270 | 37 | 218 | p24: plant transcriptional regulator PBF-2 |
Search in ModeBase |
Expression -- UniGene ? help Back to Top | ||||||
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UniGene ID | E-value | Expressed in | ||||
Os.8272 | 0.0 | callus| panicle| stem |
Expression -- Microarray ? help Back to Top | ||||||
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Source | ID | E-value | ||||
GEO | 297605165 | 0.0 | ||||
Expression Atlas | Q5VP52 | - |
Functional Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | Single-stranded DNA and RNA binding protein that maintains plastid genome stability by preventing break-induced and short homology-dependent illegitimate recombinations. Functions in RNA metabolism and is involved in the maturation of the atpF and 23S ribosomal RNAs. {ECO:0000269|PubMed:18676978, ECO:0000269|PubMed:19666500}. |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | LOC_Os06g05350.1 |
Regulation -- PlantRegMap ? help Back to Top | ||||||
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Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | - |
Phenotype -- Mutation ? help Back to Top | ||||||
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Source | ID | |||||
RiceGE | Os06g05350 |
Annotation -- Nucleotide ? help Back to Top | ||||||
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Source | Hit ID | E-value | Description | |||
GenBank | CT836194 | 0.0 | CT836194.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCEA048P18, full insert sequence. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_015641336.1 | 0.0 | single-stranded DNA-binding protein WHY1, chloroplastic | ||||
Swissprot | B2LXS7 | 1e-141 | WHY1_MAIZE; Single-stranded DNA-binding protein WHY1, chloroplastic | ||||
TrEMBL | A0A0E0HL11 | 0.0 | A0A0E0HL11_ORYNI; Uncharacterized protein | ||||
TrEMBL | A0A0E0PTG9 | 0.0 | A0A0E0PTG9_ORYRU; Uncharacterized protein | ||||
TrEMBL | Q5VP52 | 0.0 | Q5VP52_ORYSJ; Os06g0145800 protein | ||||
STRING | ORUFI06G03010.1 | 0.0 | (Oryza rufipogon) | ||||
STRING | OS06T0145800-00 | 0.0 | (Oryza sativa) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Monocots | OGMP3012 | 38 | 85 | Representative plant | OGRP2316 | 16 | 35 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT2G02740.2 | 2e-96 | ssDNA-binding transcriptional regulator |
Link Out ? help Back to Top | |
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Phytozome | LOC_Os06g05350.1 |
Entrez Gene | 4340109 |
Publications ? help Back to Top | |||
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