PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID mrna00901.1-v1.0-hybrid
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family bHLH
Protein Properties Length: 1303aa    MW: 144520 Da    PI: 5.5669
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
mrna00901.1-v1.0-hybridgenomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH11.90.000414244581655
                              HHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                      HLH  16 iNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                              + +++  L++++ +      +K + a++L +A++YIk Lq
  mrna00901.1-v1.0-hybrid 424 VADKITALQQIVSPF-----GKTDTASVLYEAIQYIKFLQ 458
                              568899999999998.....8******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088810.074408457IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474594.32E-8423471IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.103.7E-7424465IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000830.00639426462No hitNo description
SuperFamilySSF525401.36E-41711897IPR027417P-loop containing nucleoside triphosphate hydrolase
SMARTSM004875.1E-32719924IPR014001Helicase superfamily 1/2, ATP-binding domain
Gene3DG3DSA:3.40.50.3001.0E-22723908IPR027417P-loop containing nucleoside triphosphate hydrolase
PROSITE profilePS5119218.922736914IPR014001Helicase superfamily 1/2, ATP-binding domain
PfamPF001764.7E-497431058IPR000330SNF2-related, N-terminal domain
CDDcd000466.02E-18744896No hitNo description
SuperFamilySSF525401.92E-60855898IPR027417P-loop containing nucleoside triphosphate hydrolase
SuperFamilySSF525401.36E-41927978IPR027417P-loop containing nucleoside triphosphate hydrolase
SuperFamilySSF525401.92E-60935941IPR027417P-loop containing nucleoside triphosphate hydrolase
SuperFamilySSF525401.92E-6011181282IPR027417P-loop containing nucleoside triphosphate hydrolase
Gene3DG3DSA:3.40.50.3002.1E-2111261277IPR027417P-loop containing nucleoside triphosphate hydrolase
CDDcd000791.31E-2511261248No hitNo description
PfamPF002712.8E-1811281240IPR001650Helicase, C-terminal
PROSITE profilePS5119416.04111311293IPR001650Helicase, C-terminal
SMARTSM004905.7E-2011571240IPR001650Helicase, C-terminal
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006974Biological Processcellular response to DNA damage stimulus
GO:0071494Biological Processcellular response to UV-C
GO:0005524Molecular FunctionATP binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009005anatomyroot
PO:0007134developmental stagesporophyte vegetative stage
Sequence ? help Back to Top
Protein Sequence    Length: 1303 aa     Download sequence    Send to blast
MAADQCRLDS TVNCVVISSS TQPNWWDHDH LHAAAAAAGA GSHLSASSWP WQRQQQQQQQ  60
QKPNPNSNSS CDEDVSISST SFTNASNHSS LSVDSSRRLV DQRSASSNDD LNNIGEQVSD  120
NQIWSHVLLS AGNNGLNGSM THDVGENFLD ALSSKNLTNT AMYDPACDYL KKLDNASSNW  180
EFTNSSTTAA TMHASNLNNF ERQININGSF SNENLSNLVS TWSIAPPEPQ LVSSPFFNNL  240
PHQVSCYGAH NNLMKVESAA QLAGANIHGR PFSSENGSNI DYQIGLNNAM AADNNYYGSG  300
NGLVMPDSYS SSNSARSFTD VISFNSRLGK PLIDHVHHAQ KPSNFKSSIN LSDNTCKKQG  360
LQTSSPVKMS GRGQGTANES AGKKKRTEDS STSSETVLKK PKQETSAANS SSSSVKMQAP  420
KVKVADKITA LQQIVSPFGK TDTASVLYEA IQYIKFLQDQ IHVQLSSSPY LKTNTHKQDS  480
WGKLDQIRGD HQVKMDLKSR GLCLVPTSCT PQLYSNSQSP ISDVMKRSLD DYEISDDEWE  540
EDHASSFKPS RVLNNKPPPR APPPPAIESF AYKRGRASSA DDADFVVDIS DGSDDDCVEI  600
KDDDLEDDDV EEEVVRSRPV TRGRRFVVED EDSDGDWAEL ESSSEEEEEE EAEAVGDDDV  660
VGRALQKCAK ISADLKRELH GSSAAATASD RYAEVDASSV RIVTQDDINE ACRSDQSDFL  720
PVLKPYQLVG VNFLLLLYRK GIGGAILADE MGLGKTIQAV TYLMLLKHLH KDPGPHLIVC  780
PASVLENWER ELKKWCPSFS VLQYHGAARS AYSRELTSLA KAGMPPPFNV ILVCYSLFER  840
HSAQQKDDRK ILKRWRWSCV LMDEAHALKD KNSYRWKNLM SVARSANQRL MLTGTPLQND  900
LHASFIVLVT PLSLGLDTLS RTLSSHLLFL SELWSMLEFI MPDLFTTEDV DLKKLLSTAD  960
TDLISRMKSI LGPFILRRLK SDVMQQLVPK IQRVEYVIME KEQNDAYKEA IEEYRAASRA  1020
RIAKTSQANT NSIIGVIPRR QISNYFVQFR KIANHPLLVR RIYSDEDVVR FARKLHPMGA  1080
FGFECTLDRV IEEMKSFNDF SIHRLLLSYD ITDKKGCLPD EDVMLSAKSQ ALAELLPILK  1140
QAGHRVLIFS QWTSMLDILE WALDVIGVTY RRLDGSTQVT ERQTIVDTFN NDTSIFACLL  1200
STRAGGQGLN LTGADTVVIH DMDFNPQIDR QAEDRCHRIG QTKPVTIYRL VTKGTVDENV  1260
YEIAKRKLVL DAAVLESGLE MENEGAASEK TMGEILSKLL LG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5jxr_A6e-807231278106562Chromatin-remodeling complex ATPase-like protein
5jxr_B6e-807231278106562Chromatin-remodeling complex ATPase-like protein
6ne3_W7e-82723127615466SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtDNA helicase that possesses intrinsic ATP-dependent nucleosome-remodeling activity and is both required for DNA repair and heterochromatin organization. Promotes DNA end resection of double-strand breaks (DSBs) following DNA damage: probably acts by weakening histone DNA interactions in nucleosomes flanking DSBs (By similarity). Probable chromatin remodeling factor. Probable helicase-like transcription factor involved in transcriptional gene silencing. Associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. May be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin (PubMed:25420628). {ECO:0000250|UniProtKB:P31380, ECO:0000269|PubMed:25420628, ECO:0000303|PubMed:16547115}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapmrna00901.1-v1.0-hybrid
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By UV-C illumination (PubMed:15053760). Accumulates in response to the mutagens rose Bengal (RB) and methyl methane sulfonate (MMS) (PubMed:15133154). {ECO:0000269|PubMed:15053760, ECO:0000269|PubMed:15133154}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004298634.10.0PREDICTED: protein CHROMATIN REMODELING 19
SwissprotQ9ZUL50.0CHR19_ARATH; Protein CHROMATIN REMODELING 19
TrEMBLA0A2P6R4F90.0A0A2P6R4F9_ROSCH; Putative DNA helicase chromatin remodeling SNF2 family
STRINGXP_004298634.10.0(Fragaria vesca)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G31050.15e-34bHLH family protein
Publications ? help Back to Top
  1. Filkowski J,Kovalchuk O,Kovalchuk I
    Genome stability of vtc1, tt4, and tt5 Arabidopsis thaliana mutants impaired in protection against oxidative stress.
    Plant J., 2004. 38(1): p. 60-9
    [PMID:15053760]
  2. Kovalchuk I,Abramov V,Pogribny I,Kovalchuk O
    Molecular aspects of plant adaptation to life in the Chernobyl zone.
    Plant Physiol., 2004. 135(1): p. 357-63
    [PMID:15133154]
  3. Shaked H,Avivi-Ragolsky N,Levy AA
    Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination.
    Genetics, 2006. 173(2): p. 985-94
    [PMID:16547115]
  4. Xu R,Zhang S,Huang J,Zheng C
    Genome-wide comparative in silico analysis of the RNA helicase gene family in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza sativa.
    PLoS ONE, 2013. 8(11): p. e78982
    [PMID:24265739]
  5. Han YF, et al.
    SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis.
    Cell Res., 2014. 24(12): p. 1445-65
    [PMID:25420628]