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 orange1.1g002702m
Common NameCISIN_1g002708mg
Organism
Citrus sinensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family B3
Protein Properties Length: 891aa    MW: 97733.2 Da    PI: 7.1441
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g002702mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B358.51.2e-18301401199
                        EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                        f+kvl+ sd+++ grlvlpk +ae++   ++++e+  l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+F++++  
  orange1.1g002702m 301 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLRIQDVKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRMD-P 390
                        99**************************555567778***************9989999999***9.********************876.7 PP

                        EE..EEEEE-S CS
                 B3  89 efelvvkvfrk 99 
                        e++lv++++++
  orange1.1g002702m 391 EGKLVMGFRKA 401
                        77788877765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.3E-30293404IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019368.24E-20298400IPR015300DNA-binding pseudobarrel domain
CDDcd100179.78E-23299400No hitNo description
SMARTSM010195.0E-21301402IPR003340B3 DNA binding domain
PROSITE profilePS5086311.152301402IPR003340B3 DNA binding domain
PfamPF023623.7E-16301401IPR003340B3 DNA binding domain
PROSITE profilePS5105013.603566616IPR011124Zinc finger, CW-type
PfamPF074964.5E-10571613IPR011124Zinc 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: 891 aa     Download sequence    Send to blast
MESRTCMNGK CRASSSIEWR KGWPLQSGGF AVLCDKCGSA FEKLIFCDEF HSKDSGWRKC  60
ASCSKRLHCG CIASLSLIQL LDGGGVWCIN CAKNPGLDSI PGDDPNGFGT LKTDNAGDLP  120
STSVDNQLGG SDDKFKLLQL GNSSESVGLR HLLQFRNDDL DGSFRKVKPE EAAKSDISKA  180
NIGAKDIYGP LAHTNLSITL GSPGINSNSF PSAVVDEKEH SKTSAIIHQG PKSRHLLPKP  240
PKLALATGSE ANAGISQIRV ARPPAEGRGR NQLLPRYWPR ITDQELQQLS GDSNSTIVPL  300
FEKVLSASDA GRIGRLVLPK ACAEAYFPPI SQPEGLPLRI QDVKGKEWVF QFRFWPNNNS  360
RMYVLEGVTP CIQSMQLQAG DTVTFSRMDP EGKLVMGFRK ASNAVSVQDT QPSAIPNGGH  420
SSESFFSGVF ENLSILSGYS GVLQSLKGST DPHLSALSKQ LNSPPGDINW VKSEKHEDKT  480
REGLLPPSML VPERKRSRNI GSKRKRLLID RLDVLELKLT WEEAQDMLYP PPSVMPSIVT  540
VEDHVFEEYE DPPVFGKRSI FIVRTSGGQE QWAQCDGCSK WRRLPVDVLL PPKWTCMDNV  600
WDHNRCSCSA PDELTPREVE NLLRLNKDFK KRKIATSHRL NQEHEPSGLD ALSNAAILGE  660
NMGDPGTASV ATTTKHPRHR PGCSCIVCIQ PPSGKGKHKP TCTCLVCMTV KRRFKTLMMR  720
KKKRQSEREE EVAQRNQPTW GPKEEAEVDS SSKHVSSHLD PSENEARSAN ELESKSQNNN  780
LSGKLAESSK AELDLNCHPD REEVQAGLNR VSMMKLLQVA SHPLETYLKQ NGLTSLTSDQ  840
QASSGTHAPP QAAGESEGQL NELASATQER ESGGEDNCEP VSDQIPDDPE *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A4e-692794082131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1710721KRRFKTLMMRKK
2710723KRRFKTLMMRKKKR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.52130.0callus| seed
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}.
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_006429577.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_006481190.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_006481191.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_024037446.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_024037447.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_024955576.10.0B3 domain-containing transcription repressor VAL2 isoform X1
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLA0A067FKW80.0A0A067FKW8_CITSI; Uncharacterized protein
STRINGXP_006481189.10.0(Citrus sinensis)
STRINGXP_006429577.10.0(Citrus clementina)
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]