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

Gh_D12G1408

Organism

Gossypium hirsutum

Taxonomic ID

3635

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 425aa MW: 46850 Da PI: 9.0914

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_D12G1408	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.9	3.7e-05	28	48	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++Cgk F r nL+ H r H Gh_D12G1408 28 CEICGKGFQRDQNLQLHRRGH 48 *******************88 PP
2	zf-C2H2	12.3	0.00053	102	124	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k + +s+ k H +t+ Gh_D12G1408 102 WKCDKCSKQYAVQSDWKAHSKTC 124 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	3.6E-5	25	48	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.93E-6	25	48	No hit	No description
PROSITE profile	PS50157	11.489	26	48	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	28	48	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.3E-4	90	123	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.93E-6	97	122	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 425 aa Download sequence Send to blast
MIWVIADPEA EVIALSPKTL MATNRFLCEI CGKGFQRDQN LQLHRRGHNL PWKLKQRSTK 60 EVRKRVYVCP EKTCVHHHPS RALGDLTGIK KHFCRKHGEK KWKCDKCSKQ YAVQSDWKAH 120 SKTCGTREYK CDCGTLFSSR RDNFITHRAF CDALAEETAR VNAASSMHSN INHHLMGNQI 180 GPPMAQHFPP IFKPISSNNV TIDQTSCGLS LWMGQASQFH DSIPKSLQEI HQFGSVISGS 240 IYSDPLVSIS NPPASGYHLN WVLGNKVSPS HAEELTSTSL PLNNVKENGA RLVSVPSLFS 300 TQKLHSHQTT SANMSATALL QKAAQIGATS TDASFLGSLG TKCSISQIQD GNKYSGLYVS 360 NTPPTSFGSD LENSANDISN LNQLQMQPAK RQRLQNEDSS GGQTRDFLGV GVLPICHPSS 420 INGWT

Sequence ? help Back to Top

Protein Sequence Length: 425 aa Download sequence Send to blast

MIWVIADPEA EVIALSPKTL MATNRFLCEI CGKGFQRDQN LQLHRRGHNL PWKLKQRSTK  60
EVRKRVYVCP EKTCVHHHPS RALGDLTGIK KHFCRKHGEK KWKCDKCSKQ YAVQSDWKAH  120
SKTCGTREYK CDCGTLFSSR RDNFITHRAF CDALAEETAR VNAASSMHSN INHHLMGNQI  180
GPPMAQHFPP IFKPISSNNV TIDQTSCGLS LWMGQASQFH DSIPKSLQEI HQFGSVISGS  240
IYSDPLVSIS NPPASGYHLN WVLGNKVSPS HAEELTSTSL PLNNVKENGA RLVSVPSLFS  300
TQKLHSHQTT SANMSATALL QKAAQIGATS TDASFLGSLG TKCSISQIQD GNKYSGLYVS  360
NTPPTSFGSD LENSANDISN LNQLQMQPAK RQRLQNEDSS GGQTRDFLGV GVLPICHPSS  420
INGWT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-33	98	165	3	69	Zinc finger protein JACKDAW
5b3h_F	1e-33	98	165	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:25829440}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269\|PubMed:21935722}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	KT889665	6e-79	KT889665.1 Corchorus olitorius cultivar Sudan Green microsatellite JROm311 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016735900.1	0.0	PREDICTED: zinc finger protein NUTCRACKER-like, partial
Swissprot	Q9ZWA6	1e-140	IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBL	A0A2P5S255	0.0	A0A2P5S255_GOSBA; Uncharacterized protein
STRING	Gorai.008G155300.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3710	26	60

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.1	1e-142	C2H2 family protein

Publications ? help Back to Top
Muñoz-Strale D,León G Identification of two highly specific pollen promoters using transcriptomic data. Plant Physiol. Biochem., 2014. 83: p. 292-9 [PMID:25208507] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]