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

Cotton_A_04150_BGI-A2_v1.0

Organism

Gossypium arboreum

Taxonomic ID

29729

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

Protein Properties

Length: 865aa MW: 95333.4 Da PI: 7.1179

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cotton_A_04150_BGI-A2_v1.0	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	59.6	5.6e-19	333	432	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-E CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDf 79 f+kvl+ sd+++ grlvlpk +ae++ +++ e+ l+++d +g++W++++++ +++s++yvl+ G ++ +L++gD+ Cotton_A_04150_BGI-A2_v1.0 333 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGLPLRIQDVNGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLRAGDT 414 99************************555556677***********99899999999.************* PP EEEEE-SSSEE..EEEEE- CS B3 80 vvFkldgrsefelvvkvfr 98 v+F++++ +++lv+++++ Cotton_A_04150_BGI-A2_v1.0 415 VTFSRID-PGGKLVMGFRK 432 **887.77777777765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.84E-21	330	433	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.8E-30	330	435	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.68E-24	331	432	No hit	No description
PROSITE profile	PS50863	11.152	333	434	IPR003340	B3 DNA binding domain
SMART	SM01019	2.5E-23	333	433	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.4E-16	333	432	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.769	561	611	IPR011124	Zinc finger, CW-type
Pfam	PF07496	2.3E-11	566	608	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:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:2000034	Biological Process	regulation of seed maturation
GO:0005634	Cellular Component	nucleus
GO:0005739	Cellular Component	mitochondrion
GO:0003677	Molecular Function	DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 865 aa Download sequence Send to blast
MGSKICMNSS CGAATSNEWK KGWPLRSGGF AHLCYPCGSA YEDGVYCDTF HLEESGWREC 60 RICGNHLHCG CIASNYLLEL LDYGGVGCMS CAKSSRLHSV KRIQTHGDEI PEGVGAVPMN 120 NAGSSAVEGK AVSDHVDERT LAPLCKSMEA NECNLLPQSQ RGDANASLVQ HRGEEVICPT 180 EKVGAGFSNA TQPYVRPANF AKLDNARPAL DFRDIQDSLP QPYLSMSLGG SSANPNFLLP 240 FSGGLADGKE PSKTWSSFQQ GQQSRRILPK PSKNGLTTSS ELNKGMIPQA RITRPPIEGR 300 GKNHLLPRYW PRITDQELQK LSGDLKSTIV PLFEKVLSAS DAGRIGRLVL PKACAEAYFP 360 PISQSEGLPL RIQDVNGKEW TFQFRFWPNN NSRMYVLEGV TPCIQSMQLR AGDTVTFSRI 420 DPGGKLVMGF RKAANSDTQT PKGGKDLLGN ALSEHFGLPD GNISRSRDEN HGVRANENSG 480 HQLAMNAEKK KTRNIGSKSK RLLMHSVDAL ELRLTWEEAQ DLLRPPPSAR PSIVTIEDHE 540 FEEYDEPPVF GKRTIFGAWP SGEQEQWAQC DDCSKWRRLP VDVLLPSKWT CSDNVWDSSR 600 CACSAPEEIS PKELENILKV GTDLKKTKVQ EGPKVAPEPE PTGLDALASA AVLGDKMGDV 660 GESSVGATTK HPRHRPGCTC IVCIQPPSGK GKHKANCTCN VCLTVKRRFK TLMLRKKKRQ 720 SEREAEISER DNKKQMDETE LKDTRNDHSE NEGSRSRIEG EVAEASTGEI DLNCHPIRED 780 VQLGGGLNMM SFVEATSLPV KNYIKQNGIE SLKTEQQQQG SLGSHFQSEA NRENERPLSD 840 EEFLASVGWE RVGHKEPSLE RNSLQ

Sequence ? help Back to Top

Protein Sequence Length: 865 aa Download sequence Send to blast

MGSKICMNSS CGAATSNEWK KGWPLRSGGF AHLCYPCGSA YEDGVYCDTF HLEESGWREC  60
RICGNHLHCG CIASNYLLEL LDYGGVGCMS CAKSSRLHSV KRIQTHGDEI PEGVGAVPMN  120
NAGSSAVEGK AVSDHVDERT LAPLCKSMEA NECNLLPQSQ RGDANASLVQ HRGEEVICPT  180
EKVGAGFSNA TQPYVRPANF AKLDNARPAL DFRDIQDSLP QPYLSMSLGG SSANPNFLLP  240
FSGGLADGKE PSKTWSSFQQ GQQSRRILPK PSKNGLTTSS ELNKGMIPQA RITRPPIEGR  300
GKNHLLPRYW PRITDQELQK LSGDLKSTIV PLFEKVLSAS DAGRIGRLVL PKACAEAYFP  360
PISQSEGLPL RIQDVNGKEW TFQFRFWPNN NSRMYVLEGV TPCIQSMQLR AGDTVTFSRI  420
DPGGKLVMGF RKAANSDTQT PKGGKDLLGN ALSEHFGLPD GNISRSRDEN HGVRANENSG  480
HQLAMNAEKK KTRNIGSKSK RLLMHSVDAL ELRLTWEEAQ DLLRPPPSAR PSIVTIEDHE  540
FEEYDEPPVF GKRTIFGAWP SGEQEQWAQC DDCSKWRRLP VDVLLPSKWT CSDNVWDSSR  600
CACSAPEEIS PKELENILKV GTDLKKTKVQ EGPKVAPEPE PTGLDALASA AVLGDKMGDV  660
GESSVGATTK HPRHRPGCTC IVCIQPPSGK GKHKANCTCN VCLTVKRRFK TLMLRKKKRQ  720
SEREAEISER DNKKQMDETE LKDTRNDHSE NEGSRSRIEG EVAEASTGEI DLNCHPIRED  780
VQLGGGLNMM SFVEATSLPV KNYIKQNGIE SLKTEQQQQG SLGSHFQSEA NRENERPLSD  840
EEFLASVGWE RVGHKEPSLE RNSLQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	4e-70	311	436	2	127	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	705	716	KRRFKTLMLRKK
2	705	718	KRRFKTLMLRKKKR

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 VAL2/HSL1. {ECO:0000269\|PubMed:15894743, ECO:0000269\|PubMed:17158584, ECO:0000269\|PubMed:17267611}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JX581478	3e-73	JX581478.1 Gossypium hirsutum clone NBRI_GE14122 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017642000.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A1U8PZU6	0.0	A0A1U8PZU6_GOSHI; B3 domain-containing transcription repressor VAL1-like
STRING	Gorai.003G152700.1	0.0	(Gossypium raimondii)

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
AT2G30470.1	0.0	high-level expression of sugar-inducible gene 2

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