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

WALNUT_00015545-RA

Organism

Juglans regia

Taxonomic ID

51240

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Juglandaceae; Juglans

Family

Protein Properties

Length: 900aa MW: 99519 Da PI: 6.1953

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
WALNUT_00015545-RA	genome	JHU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	58	1.7e-18	311	411	1	99
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++++ WALNUT_00015545-RA 311 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGLPLRIQDVKGNDWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRID- 399 99************************555556677***********99899999999.*******************887. PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 +++lv++++++ WALNUT_00015545-RA 400 PGGKLVMGFRKA 411 788888887765 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-29	307	418	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	9.81E-20	308	410	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.16E-22	309	410	No hit	No description
SMART	SM01019	3.0E-21	311	412	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.5E-16	311	410	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.842	311	412	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.559	576	626	IPR011124	Zinc finger, CW-type
Pfam	PF07496	3.4E-11	581	623	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: 900 aa Download sequence Send to blast
MGPKICMNAS CGATSTHEWK TGWPLRSGGF ADLCHNCGSA YEDLVFCDMF HSEETGWREC 60 SLCNKRVHCG CIISKPLYEC LDFGGVGCIS CAEGPGLYPI WRGEFPNGFG SLTVKNAGDS 120 LSPPVEKRLV TGDEGKLMQL CRIVEEANEP NLLPKSQRGE ANVSQVGTGF SSVIQPSIGL 180 VTFAKPDNSR QILEGKDVQE SLAQPPLNMS LGTPNFVLPF SSGVVDGREQ SKTSSPCQQG 240 QRSRPILPKP MKTGLTASSE TNKSVVQMRI ARPPTEGRGK NQLLPRYWPR ITDQELEQLS 300 GDLNSTIVPL FEKVLSASDA GRIGRLVLPK ACAEAYFPPI SQSEGLPLRI QDVKGNDWTF 360 QFRFWPNNNS RMYVLEGVTP CIQSMQLQAG DTVTFSRIDP GGKLVMGFRK ASNTEDTQDA 420 QTSALLSDTL SRETSFSGVI ENLPSRSVFS GLFQTMKGSK EHHQNASCEN LNLVDEDIAL 480 HNSDNYRGRM NEDSPRQPMQ IPEKKRTRNI GSKSKRLLMY SEEALELRFT WEEAQDLLRP 540 PPSLKPSIVT IEGHDFEEYD EPPVFGKRTV YTTLPSRGRE QWAQCDDCSK WRRLPVDVLL 600 PPKWVCSENV WDSSRCSCSD PEEISLKQLE NFLKASKGSK ILPGFFQPSV KSSSDFKKRR 660 SAESHKSVQE CEPSGLDALA SAAVLGENVG DTGEPSVGAT TKHPRHRPGC TCIVCIQPPS 720 GKGKHKSTCT CNVCMTVKRR FKTLMLRKKK SQSEGAETAQ KDDDYNRDES EMNGPSRDGH 780 LPMIYLGNEA SHSGNQAEEA ESSNGKLDLN CHPNRDDMQL DLEVPGMSLL SLVQAASLPL 840 EDFMKQRRVP SLTCEQQGSP GIYTQVTEEN ERPLLNEGGL ASEVWERESS RDHGGYHESN

Sequence ? help Back to Top

Protein Sequence Length: 900 aa Download sequence Send to blast

MGPKICMNAS CGATSTHEWK TGWPLRSGGF ADLCHNCGSA YEDLVFCDMF HSEETGWREC  60
SLCNKRVHCG CIISKPLYEC LDFGGVGCIS CAEGPGLYPI WRGEFPNGFG SLTVKNAGDS  120
LSPPVEKRLV TGDEGKLMQL CRIVEEANEP NLLPKSQRGE ANVSQVGTGF SSVIQPSIGL  180
VTFAKPDNSR QILEGKDVQE SLAQPPLNMS LGTPNFVLPF SSGVVDGREQ SKTSSPCQQG  240
QRSRPILPKP MKTGLTASSE TNKSVVQMRI ARPPTEGRGK NQLLPRYWPR ITDQELEQLS  300
GDLNSTIVPL FEKVLSASDA GRIGRLVLPK ACAEAYFPPI SQSEGLPLRI QDVKGNDWTF  360
QFRFWPNNNS RMYVLEGVTP CIQSMQLQAG DTVTFSRIDP GGKLVMGFRK ASNTEDTQDA  420
QTSALLSDTL SRETSFSGVI ENLPSRSVFS GLFQTMKGSK EHHQNASCEN LNLVDEDIAL  480
HNSDNYRGRM NEDSPRQPMQ IPEKKRTRNI GSKSKRLLMY SEEALELRFT WEEAQDLLRP  540
PPSLKPSIVT IEGHDFEEYD EPPVFGKRTV YTTLPSRGRE QWAQCDDCSK WRRLPVDVLL  600
PPKWVCSENV WDSSRCSCSD PEEISLKQLE NFLKASKGSK ILPGFFQPSV KSSSDFKKRR  660
SAESHKSVQE CEPSGLDALA SAAVLGENVG DTGEPSVGAT TKHPRHRPGC TCIVCIQPPS  720
GKGKHKSTCT CNVCMTVKRR FKTLMLRKKK SQSEGAETAQ KDDDYNRDES EMNGPSRDGH  780
LPMIYLGNEA SHSGNQAEEA ESSNGKLDLN CHPNRDDMQL DLEVPGMSLL SLVQAASLPL  840
EDFMKQRRVP SLTCEQQGSP GIYTQVTEEN ERPLLNEGGL ASEVWERESS RDHGGYHESN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	1e-71	289	418	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	737	748	KRRFKTLMLRKK

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_018835704.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X1
Refseq	XP_018835705.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X1
Swissprot	Q6Z3U3	0.0	Y7797_ORYSJ; B3 domain-containing protein Os07g0679700
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A2I4FVM7	0.0	A0A2I4FVM7_JUGRE; B3 domain-containing transcription repressor VAL1-like isoform X1
STRING	XP_010108467.1	0.0	(Morus notabilis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF10323	30	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
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]