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

Gorai.005G004300.1

Common Name

B456_005G004300, LOC105796278

Organism

Gossypium raimondii

Taxonomic ID

29730

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: 905aa MW: 99520.1 Da PI: 7.0662

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.005G004300.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	58.8	9.4e-19	321	420	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+kvl+ sd+++ grlvlpk +ae++ ++++e+ l+++d +g++W +++++ +++s++yvl+ G ++ +L++gD+v+F++++ Gorai.005G004300.1 321 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLRIQDVKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLRAGDTVTFSRKD- 409 99************************555567778***********99899999999.*******************654. PP SEE..EEEEE- CS B3 88 sefelvvkvfr 98 e++lv+++++ Gorai.005G004300.1 410 PEGKLVMGFRK 420 88888888776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.4E-30	313	430	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.22E-19	318	420	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.71E-22	319	420	No hit	No description
SMART	SM01019	4.3E-21	321	421	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.138	321	422	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.0E-16	321	420	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.002	586	636	IPR011124	Zinc finger, CW-type
Pfam	PF07496	3.7E-11	591	633	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: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: 905 aa Download sequence Send to blast
MALKSCMNVL CGASTSIEWR NGWTLRSGDF ANLCDKCGSA YEQSIFCDVF HSKDSGWRDC 60 NSCGKPLHCG CIASRFLLEL LDGGGINCVS CAKKSGFNHM IEDEKPNGFG MVKADAGQLH 120 STSADNQLSG ASIENLQLMQ LSNNAESIGL RQLLQLHNDD SSGSLGQMKQ DEFLPPPREI 180 GSTCLTSINQ ASNGSVEAVK PTTSKVNIFD SLPQTNLSIS LGGSLGNQNG FPSSVVDEKS 240 KMSSVLQQAS KSRHLLPKPP RSVLATGLEM NAGTVPQIRV ARPPAEGRGR NQLLPRYWPR 300 ITDQELQQIS GDSNSTIVPL FEKVLSASDA GRIGRLVLPK ACAEAYFPPI SQPEGLPLRI 360 QDVKGKEWVF QFRFWPNNNS RMYVLEGVTP CIQSMQLRAG DTVTFSRKDP EGKLVMGFRK 420 ATNTAVVQET LPPAIPNGTL SSESYFSGVF ENLPIISGYS GLLQSLKGSA DPHLNGLSKH 480 SSLAGGDISG HKSDMHEDRI REDLLLTSML TPERKRTRNI GSKSKRLLID SQDALELKLT 540 WEEAQDLLHP PPSIKPSIVT IEDHDFEEYD EPPVFGKRSI FAVRSTGGQE QWAQCDNCSK 600 WRRVPVDALL PPKWTCADNN WDQSRSSCSL PDELTPRELE ILLRLNTDFT KRRIIAFHRQ 660 TQEYESSPGL NALANAAILG DNVADSGTTS VATTTKHPRH RPGCSCIVCI QPPSGKGKHK 720 PTCTCNVCLT VKRRFKTLMM RKKKRQSERE AEIALRNQQA WGPREEAEVE SSSKHVSPHH 780 DPSENEARSV NKLESKNQSN NNKLVSKLVE ANKGRIDLNC DPCRDDDSQF GSSTRMSMMN 840 LLHVASLPLE TYLKENGLTS LVSDQQAIST SHAPPQTGNT SEPYDDQCSH SATEEHETRD 900 EVNT*

Sequence ? help Back to Top

Protein Sequence Length: 905 aa Download sequence Send to blast

MALKSCMNVL CGASTSIEWR NGWTLRSGDF ANLCDKCGSA YEQSIFCDVF HSKDSGWRDC  60
NSCGKPLHCG CIASRFLLEL LDGGGINCVS CAKKSGFNHM IEDEKPNGFG MVKADAGQLH  120
STSADNQLSG ASIENLQLMQ LSNNAESIGL RQLLQLHNDD SSGSLGQMKQ DEFLPPPREI  180
GSTCLTSINQ ASNGSVEAVK PTTSKVNIFD SLPQTNLSIS LGGSLGNQNG FPSSVVDEKS  240
KMSSVLQQAS KSRHLLPKPP RSVLATGLEM NAGTVPQIRV ARPPAEGRGR NQLLPRYWPR  300
ITDQELQQIS GDSNSTIVPL FEKVLSASDA GRIGRLVLPK ACAEAYFPPI SQPEGLPLRI  360
QDVKGKEWVF QFRFWPNNNS RMYVLEGVTP CIQSMQLRAG DTVTFSRKDP EGKLVMGFRK  420
ATNTAVVQET LPPAIPNGTL SSESYFSGVF ENLPIISGYS GLLQSLKGSA DPHLNGLSKH  480
SSLAGGDISG HKSDMHEDRI REDLLLTSML TPERKRTRNI GSKSKRLLID SQDALELKLT  540
WEEAQDLLHP PPSIKPSIVT IEDHDFEEYD EPPVFGKRSI FAVRSTGGQE QWAQCDNCSK  600
WRRVPVDALL PPKWTCADNN WDQSRSSCSL PDELTPRELE ILLRLNTDFT KRRIIAFHRQ  660
TQEYESSPGL NALANAAILG DNVADSGTTS VATTTKHPRH RPGCSCIVCI QPPSGKGKHK  720
PTCTCNVCLT VKRRFKTLMM RKKKRQSERE AEIALRNQQA WGPREEAEVE SSSKHVSPHH  780
DPSENEARSV NKLESKNQSN NNKLVSKLVE ANKGRIDLNC DPCRDDDSQF GSSTRMSMMN  840
LLHVASLPLE TYLKENGLTS LVSDQQAIST SHAPPQTGNT SEPYDDQCSH SATEEHETRD  900
EVNT*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	5e-68	299	428	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	731	742	KRRFKTLMMRKK
2	731	744	KRRFKTLMMRKKKR

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}.

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	JX576979	2e-74	JX576979.1 Gossypium hirsutum clone NBRI_GE8713 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012481341.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL2-like isoform X1
Refseq	XP_012481342.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL2-like isoform X1
Swissprot	Q5CCK4	0.0	VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBL	A0A0D2R709	0.0	A0A0D2R709_GOSRA; Uncharacterized protein
STRING	Gorai.005G004300.1	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
AT4G32010.1	0.0	HSI2-like 1

Link Out ? help Back to Top
Phytozome	Gorai.005G004300.1
Entrez Gene	105796278

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] 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]