PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

676740624

Organism

Sisymbrium irio

Taxonomic ID

3730

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium

Family

Protein Properties

Length: 776aa MW: 85504.3 Da PI: 7.3775

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
676740624	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	57.8	2e-18	322	421	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkv 96 f+kvl+ sd+++ grlvlpk +ae++ ++++e+ l+++d +g++W +++++ +++s++yvl+ G ++ +L++gD+v+F++++ e++lv++ 676740624 322 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLKIQDIKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRTE-PEGKLVMGY 419 99************************555566778***********99899999999.*******************654.777777776 PP E- CS B3 97 fr 98 ++ 676740624 420 RK 421 65 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.0E-29	317	425	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	5.62E-20	319	422	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.64E-22	320	421	No hit	No description
PROSITE profile	PS50863	11.053	322	423	IPR003340	B3 DNA binding domain
SMART	SM01019	4.9E-20	322	422	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.3E-15	322	421	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.769	550	600	IPR011124	Zinc finger, CW-type
Pfam	PF07496	5.4E-13	555	597	IPR011124	Zinc finger, CW-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010030	Biological Process	positive regulation of seed germination
GO:2000034	Biological Process	regulation of seed maturation
GO:0003677	Molecular Function	DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 776 aa Download sequence Send to blast
MESTKVCMNA QCGSTSTSGE WKRGWPMRSG ELVSLCDKCG SAYEQLIFCQ VFHAEESGWR 60 ECSSCDKRLH CGCIASRFMM ELLDNGGVTC ISCAKKSGLF SVRIFSHPCI NFLIQGCFLG 120 LGFCVNTLMQ PLLQMNVSHE SNGRDFPSSA SAEHVGSVLE RTNLKHFLHF QRIGATQSFL 180 QMKQEESLLP ARLEALRHKS EKKELQELST QPNLSISLGP ALMTSPFHDT VVDDRSKTTP 240 IFQLGPRSRQ LLPKPANSAP TAAGMEPNGS LVSQIHVARP PPEGRGKTQL LPRYWPRITD 300 QELQQLSGQY PHLSNSKIIP LFEKVLSASD AGRIGRLVLP KACAEAYFPP ISQPEGLPLK 360 IQDIKGKEWV FQFRFWPNNN SRMYVLEGVT PCIQSMQLQA GDTVTFSRTE PEGKLVMGYR 420 KATNSTAAQM FKGSSEPNLN MFSNNLSPGG DINWSKLDKP EDMAKDNLLL QPSLISARKR 480 VRNIGTKSKR LLIDSVDVLE LRLTWEEAQE LLRPPQSAKP SICTVDDHDF EEYDEPPVFG 540 KRTVFVARQT GEQEQWVQCD ACAKWRRLPV DTLLPPKWLC SDNLLDPGRA SCSAPDELTP 600 REQDTLVRLS KEFKRRRLAS SNEKLNQEQE GSALDTLANA AVTTPGGQGD TAVAATTKHP 660 RHRAGCSCIV CSQPPSGKGK HKPSCTCTTE AESIPVVEPV AGGNIDLNSD PGASRVSMMS 720 LLQAATFPLE AYLKQKAVPN TAAEQQSSDM VSTEHGSSSA AQELDRDTSV APEPMN

Sequence ? help Back to Top

Protein Sequence Length: 776 aa Download sequence Send to blast

MESTKVCMNA QCGSTSTSGE WKRGWPMRSG ELVSLCDKCG SAYEQLIFCQ VFHAEESGWR  60
ECSSCDKRLH CGCIASRFMM ELLDNGGVTC ISCAKKSGLF SVRIFSHPCI NFLIQGCFLG  120
LGFCVNTLMQ PLLQMNVSHE SNGRDFPSSA SAEHVGSVLE RTNLKHFLHF QRIGATQSFL  180
QMKQEESLLP ARLEALRHKS EKKELQELST QPNLSISLGP ALMTSPFHDT VVDDRSKTTP  240
IFQLGPRSRQ LLPKPANSAP TAAGMEPNGS LVSQIHVARP PPEGRGKTQL LPRYWPRITD  300
QELQQLSGQY PHLSNSKIIP LFEKVLSASD AGRIGRLVLP KACAEAYFPP ISQPEGLPLK  360
IQDIKGKEWV FQFRFWPNNN SRMYVLEGVT PCIQSMQLQA GDTVTFSRTE PEGKLVMGYR  420
KATNSTAAQM FKGSSEPNLN MFSNNLSPGG DINWSKLDKP EDMAKDNLLL QPSLISARKR  480
VRNIGTKSKR LLIDSVDVLE LRLTWEEAQE LLRPPQSAKP SICTVDDHDF EEYDEPPVFG  540
KRTVFVARQT GEQEQWVQCD ACAKWRRLPV DTLLPPKWLC SDNLLDPGRA SCSAPDELTP  600
REQDTLVRLS KEFKRRRLAS SNEKLNQEQE GSALDTLANA AVTTPGGQGD TAVAATTKHP  660
RHRAGCSCIV CSQPPSGKGK HKPSCTCTTE AESIPVVEPV AGGNIDLNSD PGASRVSMMS  720
LLQAATFPLE AYLKQKAVPN TAAEQQSSDM VSTEHGSSSA AQELDRDTSV APEPMN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-66	296	429	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	613	617	KRRRL

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional 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
Source	Link
PlantRegMap	676740624

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB206554	0.0	AB206554.1 Arabidopsis thaliana HSI2-L1 mRNA for transcription factor B3-EAR motif family, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010432783.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_010432784.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_010432785.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL2 isoform X1
Swissprot	Q5CCK4	0.0	VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBL	A0A1J3CN34	0.0	A0A1J3CN34_NOCCA; B3 domain-containing transcription repressor VAL2
STRING	XP_010432783.1	0.0	(Camelina sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7203	26	39

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G32010.1	0.0	HSI2-like 1

Publications ? help Back to Top
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] 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] 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] Li C,Cui Y A DNA element that remembers winter. Nat. Genet., 2016. 48(12): p. 1451-1452 [PMID:27898079]