PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Carubv10022654m
Common NameCARUB_v10022654mg
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: 809aa    MW: 88597.3 Da    PI: 7.9834
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10022654mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.91.9e-18306401194
                      EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 
                      f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +g++W+++++y  +++s++yvl+ G     ++  L++gD+v+F++++  ++
  Carubv10022654m 306 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVKGKEWTFQFRYwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD-PGG 397
                      99**************************666678889*****************89999999***9.********************765.666 PP

                      ..EE CS
               B3  91 elvv 94 
                      +l +
  Carubv10022654m 398 KLIM 401
                      5555 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.7E-29303415IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.22E-19303401IPR015300DNA-binding pseudobarrel domain
CDDcd100171.89E-23304401No hitNo description
PROSITE profilePS5086310.574306407IPR003340B3 DNA binding domain
PfamPF023627.3E-16306400IPR003340B3 DNA binding domain
SMARTSM010195.0E-22306406IPR003340B3 DNA binding domain
PROSITE profilePS5105012.93558608IPR011124Zinc finger, CW-type
PfamPF074969.5E-9564605IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 809 aa     Download sequence    Send to blast
MFEVKMGSKM CMNASCGTTS SVEWKKGWPL RSGLLADLCQ RCGSVYESST FCEKFHKDQS  60
GWRECYLCNK KLHCGCIASK VMIELMDYGG VGCSTCACRQ KLNFNNSGEN PGVFSRLPMK  120
SLADRQYVNG ESGMNIEGGR NEADLFSQPQ RCESQPLVMG GDKREEFIPH RGFGNLMSSE  180
NTNTGFRLDA VEMHESSPAQ PSLNMGLSVL PYSPSFSTEG IEGKKHIGAS QSNMVHCSAS  240
NILQKPSKPA MSTPPVASKS AQARIGRPPV EGRGKGHLLP RYWPKYTDKE VQQISGNLNL  300
NIVPLFEKTL SASDAGRIGR LVLPKACAEA YFPPISQSEG IPLKIQDVKG KEWTFQFRYW  360
PNNNSRMYVL EGVTPCIQSM MLQAGDTVTF SRVDPGGKLI MGSRKAANGG DIQSCGLTNG  420
TSTEDTSSSG VTENPPSING SSCPSLIPKE LNGMPENLSS PYGGNGIKNE NNGVRVADDP  480
TRVKEKKRTR TIGTKTKRLL LHSEESMELR ITWEEAQDLF RPSPSAKPTI VVIEGHEFEE  540
FDEPPVCGKK TIVTTKPSGE QERWAACDDC SKWRRLPVNA LLSLKWTCID NVWDVSRCSC  600
SAPEESLKEL ENALKAGREY KKRRTGESQA AKSEQEPSGL DALASAAVLG DTMGEPEVAT  660
TTRHPRHRAG CSCIVCIQPP SGKGRHKPNC ACTVCSTVKR RFKTLMMRRK KKQLERDGPA  720
AEEKEKKDME QAESDKNKAE EEVNTARIDL NSDPYNKEDV EAVAGEKDES RKRKIGQSSG  780
VAQEGDVVGV KVLEGEAEKI GEDPKGSS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A2e-852844132131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1698710KRRFKTLMMRRKK
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 VAL2/HSL1. {ECO:0000269|PubMed:15894743, ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10022654m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB2065530.0AB206553.1 Arabidopsis thaliana HSI2 mRNA for transcription factor B3-EAR motif, complete cds.
GenBankAY0624920.0AY062492.1 Arabidopsis thaliana putative VP1/ABI3 family regulatory protein (At2g30470; T6B20.17) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006293696.10.0B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLR0HB220.0R0HB22_9BRAS; Uncharacterized protein
STRINGXP_006293696.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69232440
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G30470.10.0high-level expression of sugar-inducible gene 2
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. Schneider A, et al.
    Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos.
    Plant J., 2016. 85(2): p. 305-19
    [PMID:26678037]
  3. 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]
  4. Qüesta JI,Song J,Geraldo N,An H,Dean C
    Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization.
    Science, 2016. 353(6298): p. 485-8
    [PMID:27471304]
  5. 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]
  6. Merini W, et al.
    The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development.
    Plant Physiol., 2017. 173(1): p. 627-641
    [PMID:27837089]
  7. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  8. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619
    [PMID:29475938]
  9. Sasnauskas G,Kauneckaite K,Siksnys V
    Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
    Nucleic Acids Res., 2018. 46(8): p. 4316-4324
    [PMID:29660015]
  10. Wu B, et al.
    Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
    Biochem. Biophys. Res. Commun., 2018. 501(2): p. 415-422
    [PMID:29733847]