PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Carubv10004194m
Common NameCARUB_v10004194mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family B3
Protein Properties Length: 776aa    MW: 85220.3 Da    PI: 7.6279
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10004194mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.74.3e-18284383198
                      EEEE-..-HHHHTT-EE--HHH.HTT....---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh....ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                      f+kvl+ sd+++ grlvlpk +ae++    ++++     l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+F++++  
  Carubv10004194m 284 FEKVLSASDAGRIGRLVLPKACAEAYfppiSLPEGL--PLKIQDIKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRTE-P 373
                      99**************************88777555..5***************9989999999***9.********************654.7 PP

                      EE..EEEEE- CS
               B3  89 efelvvkvfr 98 
                      e++lv++ ++
  Carubv10004194m 374 EGKLVMGYRK 383
                      7777777665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.104.9E-29277388IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.84E-20281384IPR015300DNA-binding pseudobarrel domain
CDDcd100171.64E-22282383No hitNo description
PROSITE profilePS5086310.955284385IPR003340B3 DNA binding domain
SMARTSM010196.9E-20284384IPR003340B3 DNA binding domain
PfamPF023622.1E-15284383IPR003340B3 DNA binding domain
PROSITE profilePS5105014.864513563IPR011124Zinc finger, CW-type
PfamPF074961.4E-13518560IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010030Biological Processpositive regulation of seed germination
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 776 aa     Download sequence    Send to blast
MESTKVCMNA LCGASSASGE WKKGWPMRSG DLASLCDKCG SAYEQSIFCQ VFHAEESGWR  60
ECNSCDKRLH CGCIASRFMM ELLDNGSVTC ISCAKKSALF SMNVSQESNG RDSSFASAEH  120
VGSVLERTNL KHLLDFQRIG PTQSSIQMKQ EESLLPSRLD ALRHKTERKE LQELSAQPNL  180
SISLGPTLMT SPFHDAVIDD RSKTTSIFQL APRSRQLLPK PANSAPTAAG MEPNGSLVSQ  240
IHVARPPPEG RGKTQLLPRY WPRITDQELQ ILSGHSNSKI IPLFEKVLSA SDAGRIGRLV  300
LPKACAEAYF PPISLPEGLP LKIQDIKGKE WVFQFRFWPN NNSRMYVLEG VTPCIQSMQL  360
QAGDTVTFSR TEPEGKLVMG YRKATNSTAT QMFKGSSEPN LNIFSNNLNP GCGDISWSKL  420
EKAEDMGKDN LFLQSSLTSS RKRVRNIGSK SKRLLIDSVD VLELKVTWDE AQELMRPPQS  480
AKPSIITLEN QDFEEYDEPP VFGKKTVFVA RQTGEQEQWV QCDACGKWRR LPVDTLLPPK  540
WLCSDNHLDP ARSSCSAPDD LSPREQDTLV RQSKEFKRRR LAASNEKLNQ SQEASAVETL  600
ANAGITTTGE QGEIAVAATT KHPRHRAGCS CIVCSQPPSG KGKHKPTCTC TVCEAVKRRF  660
RTLMMRKKNR GEAGQASQQA QSESRDETEV ESIPAAEAAS GDNIDLNSDP GGSRVSMMGL  720
LQAAAFPLEA YLKQKAISNT GGEQQSSDMV STEHGSSSAA QEQEKDTNGV HEPVS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A9e-672623912131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1576580KRRRL
2656667KRRFRTLMMRKK
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL1/HSI2. {ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10004194m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2280130.0AK228013.1 Arabidopsis thaliana mRNA for predicted protein, complete cds, clone: RAFL14-53-K16.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006283163.10.0B3 domain-containing transcription repressor VAL2
RefseqXP_023634381.10.0B3 domain-containing transcription repressor VAL2
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLR0F3W50.0R0F3W5_9BRAS; Uncharacterized protein
STRINGXP_006283163.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM72032639
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G32010.10.0HSI2-like 1
Publications ? help Back to Top
  1. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  2. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  3. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  4. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]