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

913255

Common Name

ARALYDRAFT_913255

Organism

Arabidopsis lyrata

Taxonomic ID

81972

Taxonomic Lineage

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

Family

Protein Properties

Length: 786aa MW: 86892.4 Da PI: 7.63

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
913255	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	56.7	4.3e-18	289	388	1	98
EEEE-..-HHHHTT-EE--HHH.HTT....---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh....ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 f+kvl+ sd+++ grlvlpk +ae++ ++++ l+++d +g++W +++++ +++s++yvl+ G ++ +L++gD+v+F++++ e++lv++ + 913255 289 FEKVLSASDAGRIGRLVLPKACAEAYfppiSLPEGL--PLKIQDIKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRTE-PEGKLVMGYR 387 99************************88777555..5***********99899999999.*******************654.7777777766 PP - CS B3 98 r 98 + 913255 388 K 388 5 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	6.8E-29	284	393	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	4.97E-20	286	389	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.68E-22	287	388	No hit	No description
Pfam	PF02362	2.1E-15	289	388	IPR003340	B3 DNA binding domain
SMART	SM01019	6.9E-20	289	389	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.955	289	390	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.748	518	568	IPR011124	Zinc finger, CW-type
Pfam	PF07496	4.6E-13	523	565	IPR011124	Zinc finger, CW-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010030	Biological Process	positive regulation of seed germination
GO:2000034	Biological Process	regulation of seed maturation
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 786 aa Download sequence Send to blast
MESIKVCMNA LCGAASTSGE WKKGWPMRSG DLASLCDKCG TAYEQSIFCE VFHAEESGWR 60 ECNSCDKRLH CGCIASRFMM ELLENGGVTC ISCAKKSGLF SMNVSHISNG RDFPSFASAE 120 HVGSVLERTN LKHLLHFQRI DPTQSSLQMK QEESLLPSRL DALRHKTERK ELQELSAQPN 180 LSISLGPTLM TSPFHDAAVD DRSKTNSIFQ LAPRSRQLLP KPANSAPIAA GMEPSGSLVS 240 QIHVARPPPE GRGKTQLLPR YWPRITDQEL LQLSGQYPHL SNSKIIPLFE KVLSASDAGR 300 IGRLVLPKAC AEAYFPPISL PEGLPLKIQD IKGKEWVFQF RFWPNNNSRM YVLEGVTPCI 360 QSMQLQAGDT VTFSRTEPEG KLVMGYRKAT NSTATQMFKG SSEPNLNMFS NSLNPGCGDI 420 NWSKLEKSED MAKDNLFLQS SLTSARKRVR NIGTKSKRLL IDSVDVLELK ITWEEAQELL 480 RPPQSAKPSI FTLENQDFEE YDEPPVFGKR TLFVSRQTGE QEQWVQCDAC GKWRRLPVDI 540 LLPPKWSCSD NLLDPGRSSC SAPDELSPRE QDTLVRQSKE FKRRRLASSN EKLNQSQEAS 600 ALDTLGNGGI TTTGEQEEIT VAATTKHPRH RAGCSCIVCS QPPSGKGKHK PSCTCTVCEA 660 VKRRFRTLML RKRNRGEAGQ ASQQAQSQSE CRDETEVESI PAIEPAAGEN IDLNSDPGAS 720 RVSMMRLLQA AAFPLEAYLK QKAISNTAGE QQSSDMVSTE HGSSSAAQEH EKEKDTTNGA 780 HDPVN*

Sequence ? help Back to Top

Protein Sequence Length: 786 aa Download sequence Send to blast

MESIKVCMNA LCGAASTSGE WKKGWPMRSG DLASLCDKCG TAYEQSIFCE VFHAEESGWR  60
ECNSCDKRLH CGCIASRFMM ELLENGGVTC ISCAKKSGLF SMNVSHISNG RDFPSFASAE  120
HVGSVLERTN LKHLLHFQRI DPTQSSLQMK QEESLLPSRL DALRHKTERK ELQELSAQPN  180
LSISLGPTLM TSPFHDAAVD DRSKTNSIFQ LAPRSRQLLP KPANSAPIAA GMEPSGSLVS  240
QIHVARPPPE GRGKTQLLPR YWPRITDQEL LQLSGQYPHL SNSKIIPLFE KVLSASDAGR  300
IGRLVLPKAC AEAYFPPISL PEGLPLKIQD IKGKEWVFQF RFWPNNNSRM YVLEGVTPCI  360
QSMQLQAGDT VTFSRTEPEG KLVMGYRKAT NSTATQMFKG SSEPNLNMFS NSLNPGCGDI  420
NWSKLEKSED MAKDNLFLQS SLTSARKRVR NIGTKSKRLL IDSVDVLELK ITWEEAQELL  480
RPPQSAKPSI FTLENQDFEE YDEPPVFGKR TLFVSRQTGE QEQWVQCDAC GKWRRLPVDI  540
LLPPKWSCSD NLLDPGRSSC SAPDELSPRE QDTLVRQSKE FKRRRLASSN EKLNQSQEAS  600
ALDTLGNGGI TTTGEQEEIT VAATTKHPRH RAGCSCIVCS QPPSGKGKHK PSCTCTVCEA  660
VKRRFRTLML RKRNRGEAGQ ASQQAQSQSE CRDETEVESI PAIEPAAGEN IDLNSDPGAS  720
RVSMMRLLQA AAFPLEAYLK QKAISNTAGE QQSSDMVSTE HGSSSAAQEH EKEKDTTNGA  780
HDPVN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5z28_A	1e-65	3	105	1	103	B3 domain-containing transcription repressor VAL2
5z28_B	1e-65	3	105	1	103	B3 domain-containing transcription repressor VAL2
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	581	585	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	913255

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_002869299.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_020874404.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_020874405.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_020874406.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Swissprot	Q5CCK4	0.0	VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBL	D7MAS9	0.0	D7MAS9_ARALL; Transcriptional factor B3 family protein
STRING	scaffold_700997.1	0.0	(Arabidopsis lyrata)

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

Link Out ? help Back to Top
Phytozome	913255
Entrez Gene	9305370

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]