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

Cc01_g15330

Common Name

GSCOC_T00016576001

Organism

Coffea canephora

Taxonomic ID

49390

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea

Family

Protein Properties

Length: 842aa MW: 92081.3 Da PI: 6.7962

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cc01_g15330	genome	CGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	60.6	2.7e-19	314	413	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 f+kvl+ sd+++ grlvlpk +ae++ +++ e+ ++++d +g++W++++++ +++s++yvl+ G + +L++gD+v+F++++ +++lv+ Cc01_g15330 314 FEKVLSASDAGRIGRLVLPKACAEAYfpPINQSEGLPIRIQDVKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQNMQLQAGDTVTFSRID-PGGQLVM 409 99************************666667778***********99899999999.*******************887.6666666 PP EEE- CS B3 95 kvfr 98 ++++ Cc01_g15330 410 GFRK 413 6655 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.1E-29	310	417	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	3.4E-21	312	416	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.76E-24	312	413	No hit	No description
SMART	SM01019	2.0E-22	314	414	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.2E-16	314	413	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.335	314	415	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	13.518	544	593	IPR011124	Zinc finger, CW-type
Pfam	PF07496	9.3E-10	549	590	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: 842 aa Download sequence Send to blast
MGSKICMNEV CRLTTSPEWK QGWGLKSGGF ATLCSSCGTA YENLVFCEKF HLDEDGWREC 60 KICRKRIHCG CVASKMLHEF LDFGGVGCIT CVKQMDTPSL RTVKILGDEI PNGTIGHRSF 120 DSLLQLCNNV DVNGSKKMFK PHKVGTNASL GQKKGEGTAL PFEQVNTSSP NFTPQSVGSS 180 MFVKPEISRQ NQGFKDMAES LAQPSVNFSL SNALSASGSA LPISEGIVEG SEQNRVSTAQ 240 QGQRARQILP KPPKPGSSVG SENTKGMGSQ TRIARPPAEG RGRSQLLPRY WPRITDQELQ 300 QISGDLKSTV VPLFEKVLSA SDAGRIGRLV LPKACAEAYF PPINQSEGLP IRIQDVKGKE 360 WTFQFRFWPN NNSRMYVLEG VTPCIQNMQL QAGDTVTFSR IDPGGQLVMG FRKSTTNVET 420 QDPQPSGLPN GGSPGETSYL GASDNMLAIS ENGNNGGQIH EDSSQRNILI PEKKKARNIG 480 LKNKRLLMHS DDAMELRVTW EEAQELLRPP TNSPTIIKIE DCEFEEYDEP PIFGKRTIFT 540 VQPSGQQEQW AQCDNCSKWR RLPMHVLVPA RWTCPDNAWV LNSTCSAPDD INPRELEALN 600 IASKDFKRRR IVETKVAEDY EPSGLDALAT AAVLGDNMGD LTEMSVGATT KHPRHRPGCS 660 CIVCIQPPSG KGKHPPSCKC NVCLTVKRRF KTLMMRKKKR QSDREAELLQ GKDQETPPLD 720 MSEMEGAAEQ ALLLTNHSDA ERSQNGSLME AGESNKGQLD LNCHPSREED MLAEAAAGIN 780 LATLIDAASI PLDVYMRQDG VASLSHHLLP SHAPGDGEGS LPEEGCSASA NMGPEKKGKE 840 E*

Sequence ? help Back to Top

Protein Sequence Length: 842 aa Download sequence Send to blast

MGSKICMNEV CRLTTSPEWK QGWGLKSGGF ATLCSSCGTA YENLVFCEKF HLDEDGWREC  60
KICRKRIHCG CVASKMLHEF LDFGGVGCIT CVKQMDTPSL RTVKILGDEI PNGTIGHRSF  120
DSLLQLCNNV DVNGSKKMFK PHKVGTNASL GQKKGEGTAL PFEQVNTSSP NFTPQSVGSS  180
MFVKPEISRQ NQGFKDMAES LAQPSVNFSL SNALSASGSA LPISEGIVEG SEQNRVSTAQ  240
QGQRARQILP KPPKPGSSVG SENTKGMGSQ TRIARPPAEG RGRSQLLPRY WPRITDQELQ  300
QISGDLKSTV VPLFEKVLSA SDAGRIGRLV LPKACAEAYF PPINQSEGLP IRIQDVKGKE  360
WTFQFRFWPN NNSRMYVLEG VTPCIQNMQL QAGDTVTFSR IDPGGQLVMG FRKSTTNVET  420
QDPQPSGLPN GGSPGETSYL GASDNMLAIS ENGNNGGQIH EDSSQRNILI PEKKKARNIG  480
LKNKRLLMHS DDAMELRVTW EEAQELLRPP TNSPTIIKIE DCEFEEYDEP PIFGKRTIFT  540
VQPSGQQEQW AQCDNCSKWR RLPMHVLVPA RWTCPDNAWV LNSTCSAPDD INPRELEALN  600
IASKDFKRRR IVETKVAEDY EPSGLDALAT AAVLGDNMGD LTEMSVGATT KHPRHRPGCS  660
CIVCIQPPSG KGKHPPSCKC NVCLTVKRRF KTLMMRKKKR QSDREAELLQ GKDQETPPLD  720
MSEMEGAAEQ ALLLTNHSDA ERSQNGSLME AGESNKGQLD LNCHPSREED MLAEAAAGIN  780
LATLIDAASI PLDVYMRQDG VASLSHHLLP SHAPGDGEGS LPEEGCSASA NMGPEKKGKE  840
E*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	3e-68	292	421	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	606	610	KRRRI
2	686	697	KRRFKTLMMRKK
3	686	699	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 VAL2/HSL1. {ECO:0000269\|PubMed:15894743, ECO:0000269\|PubMed:17158584, ECO:0000269\|PubMed:17267611}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027112477.1	0.0	B3 domain-containing transcription repressor VAL1-like isoform X2
Refseq	XP_027112486.1	0.0	B3 domain-containing transcription repressor VAL1-like isoform X3
Swissprot	Q6Z3U3	0.0	Y7797_ORYSJ; B3 domain-containing protein Os07g0679700
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A068U8U9	0.0	A0A068U8U9_COFCA; Uncharacterized protein
STRING	XP_009772834.1	0.0	(Nicotiana sylvestris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA1491	23	65

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
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] 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]