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

Neem_180_f_1

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

Protein Properties

Length: 905aa MW: 99513 Da PI: 6.696

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_180_f_1	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	54.8	1.7e-17	314	413	2	99
EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS B3 2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 f+vl+ sd+++ grlvlpk +ae++ ++++e+ l+++d +g++W +++++ +++s++yvl+ G ++ +L++gD+v+F++++ e++lv+ Neem_180_f_1 314 FTVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLRIQDVKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRMD-PEGKLVM 408 57899********************555567778***********99899999999.*******************876.7777888 PP EEE-S CS B3 95 kvfrk 99 +++++ Neem_180_f_1 409 GFRKA 413 77765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01019	1.7E-18	313	414	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.447	313	414	IPR003340	B3 DNA binding domain
CDD	cd10017	2.62E-20	314	412	No hit	No description
Pfam	PF02362	3.9E-15	314	413	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	7.59E-18	314	413	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	6.7E-27	315	417	IPR015300	DNA-binding pseudobarrel domain
PROSITE profile	PS51050	13.718	579	629	IPR011124	Zinc finger, CW-type
Pfam	PF07496	4.1E-11	584	626	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:2000034	Biological Process	regulation of seed maturation
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
MAREYDRGIE YGGCSELSLE QMESRTCMNE ACRASTSIEW RKGWALRSGD FAVLCDKCGS 60 VFEQLIFCDE FHSKDSGWRE CTSCGKRLHC GCIASRALIE LLDSGGVSCI NCAKKSELDL 120 VAGNEKPNGF GTLKADNASD LQSTSVDNQL GGSIKLVQLG NSSEGAGLRH LLQFRNDDPD 180 GSFGKTKLEE AAKPDVSKAD IGAKGIYESL AHTNLSITLG SPGVNSNSFP SAVVDEKEHS 240 KTSPFIQQGN RSRHLLPKPP KLALATGSEA NAAMSQVRVA RPPAEGRGRN QLLPRYWPRI 300 TDQELQQISG EYPFTVLSAS DAGRIGRLVL PKACAEAYFP PISQPEGLPL RIQDVKGKEW 360 VFQFRFWPNN NSRMYVLEGV TPCIQSMQLQ AGDTVTFSRM DPEGKLVMGF RKASSSAALQ 420 DAQPSAIPNG AHSSESFFSG VFENLSIISG YSGVLQSLKG STDPHLNALS KHLNATSGDI 480 SWVKSEKHED KPRDSLLLPS MLAPERKRSR NIGSKSKRLL IDRLDALELK LTWEEAQDML 540 RPPPTVMPSI VTIEDHAFEE YEGSGWINSS NLELLSLIFR GQEQWAQCDG CSKWRRLPID 600 VLLPPKWTCM DNAWDHSRSS CSTPDELTPR ELENLLRLHK DFKKRRIATS HRPSQEHEPS 660 GLDALSNAAI LGENMGEPGT ASVATTTKHP RHRPGCSCIV CIQPPSGKGK HKPTCTCNVC 720 MTVKRRFKTL MMRKKKRQSE REAEVAQRNQ PTWGSKEEAE VESSSKHISS HLDPSENEAR 780 SGNELESKIQ SNNMSSKLPE AGKSEIDLNC QPERDDMQAG LNRVSMMKLL QVASLPLETY 840 LKQNGLTSLM SEQQQASSAS HAPPAQATGE SDGRLNEFAS ATQDRESGGE ENCEAVSDKI 900 PDDPQ

Sequence ? help Back to Top

Protein Sequence Length: 905 aa Download sequence Send to blast

MAREYDRGIE YGGCSELSLE QMESRTCMNE ACRASTSIEW RKGWALRSGD FAVLCDKCGS  60
VFEQLIFCDE FHSKDSGWRE CTSCGKRLHC GCIASRALIE LLDSGGVSCI NCAKKSELDL  120
VAGNEKPNGF GTLKADNASD LQSTSVDNQL GGSIKLVQLG NSSEGAGLRH LLQFRNDDPD  180
GSFGKTKLEE AAKPDVSKAD IGAKGIYESL AHTNLSITLG SPGVNSNSFP SAVVDEKEHS  240
KTSPFIQQGN RSRHLLPKPP KLALATGSEA NAAMSQVRVA RPPAEGRGRN QLLPRYWPRI  300
TDQELQQISG EYPFTVLSAS DAGRIGRLVL PKACAEAYFP PISQPEGLPL RIQDVKGKEW  360
VFQFRFWPNN NSRMYVLEGV TPCIQSMQLQ AGDTVTFSRM DPEGKLVMGF RKASSSAALQ  420
DAQPSAIPNG AHSSESFFSG VFENLSIISG YSGVLQSLKG STDPHLNALS KHLNATSGDI  480
SWVKSEKHED KPRDSLLLPS MLAPERKRSR NIGSKSKRLL IDRLDALELK LTWEEAQDML  540
RPPPTVMPSI VTIEDHAFEE YEGSGWINSS NLELLSLIFR GQEQWAQCDG CSKWRRLPID  600
VLLPPKWTCM DNAWDHSRSS CSTPDELTPR ELENLLRLHK DFKKRRIATS HRPSQEHEPS  660
GLDALSNAAI LGENMGEPGT ASVATTTKHP RHRPGCSCIV CIQPPSGKGK HKPTCTCNVC  720
MTVKRRFKTL MMRKKKRQSE REAEVAQRNQ PTWGSKEEAE VESSSKHISS HLDPSENEAR  780
SGNELESKIQ SNNMSSKLPE AGKSEIDLNC QPERDDMQAG LNRVSMMKLL QVASLPLETY  840
LKQNGLTSLM SEQQQASSAS HAPPAQATGE SDGRLNEFAS ATQDRESGGE ENCEAVSDKI  900
PDDPQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	6e-61	298	420	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	723	734	KRRFKTLMMRKK
2	723	736	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006429577.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_006481190.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_006481191.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_024037446.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_024037447.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Refseq	XP_024955576.1	0.0	B3 domain-containing transcription repressor VAL2 isoform X1
Swissprot	Q5CCK4	0.0	VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBL	A0A067FKW8	0.0	A0A067FKW8_CITSI; Uncharacterized protein
STRING	XP_006481189.1	0.0	(Citrus sinensis)
STRING	XP_006429577.1	0.0	(Citrus clementina)

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

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]