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.005G198900.1

Common Name

B456_005G198900, LOC105794844

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

C2H2

Protein Properties

Length: 463aa MW: 51250.4 Da PI: 8.8778

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.005G198900.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.8	4.1e-05	60	80	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++Cgk F r nL+ H r H Gorai.005G198900.1 60 CEICGKGFQRDQNLQLHRRGH 80 *******************88 PP
2	zf-C2H2	13.5	0.00021	134	156	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Gorai.005G198900.1 134 WKCEKCSKRYAVQSDWKAHSKTC 156 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	8.24E-7	57	80	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.0E-5	57	80	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.076	58	80	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.489	58	80	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	60	80	IPR007087	Zinc finger, C2H2
SMART	SM00355	120	99	129	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.9E-5	122	155	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	8.24E-7	129	154	No hit	No description
SMART	SM00355	130	134	154	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0044212	Molecular Function	transcription regulatory region DNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 463 aa Download sequence Send to blast
MLETMAEEPV SNGFMQNPVP GSNNPPVAKR KRNLPGTPDP EAEVIALSPK TLMATNRFLC 60 EICGKGFQRD QNLQLHRRGH NLPWKLKQRT TKEVRKRVYV CPEKTCVHHH PSRALGDLTG 120 IKKHFYRKHG EKKWKCEKCS KRYAVQSDWK AHSKTCGTRE YKCDCGTLFS RRDSFITHRA 180 FCDALAEETA RVNAASSMHS LATTNFSYQL MGNPLDTGMP QHFPSIFKTI SSNDETIDQT 240 RRGFSLWMGQ APQGHDSIGK SLQEIQQFGS LNSGSMYSDP LVSTSNPPAS DYQLNWVFGN 300 KVSSGNAEDQ LTSTSLPLNN NAKENGTQLV SIPSLFSTQH QSQQTPSFSM SATALLQKAA 360 QIGATSTDTS FLGSFGTKCS NSQIQDGSQY GDLYVSNTQT TTLGRDMENS ANDISTLNQL 420 QMYPPKRRYL QNEESGGGQT RDFLGVGVQQ AICHPSSING WI*

Sequence ? help Back to Top

Protein Sequence Length: 463 aa Download sequence Send to blast

MLETMAEEPV SNGFMQNPVP GSNNPPVAKR KRNLPGTPDP EAEVIALSPK TLMATNRFLC  60
EICGKGFQRD QNLQLHRRGH NLPWKLKQRT TKEVRKRVYV CPEKTCVHHH PSRALGDLTG  120
IKKHFYRKHG EKKWKCEKCS KRYAVQSDWK AHSKTCGTRE YKCDCGTLFS RRDSFITHRA  180
FCDALAEETA RVNAASSMHS LATTNFSYQL MGNPLDTGMP QHFPSIFKTI SSNDETIDQT  240
RRGFSLWMGQ APQGHDSIGK SLQEIQQFGS LNSGSMYSDP LVSTSNPPAS DYQLNWVFGN  300
KVSSGNAEDQ LTSTSLPLNN NAKENGTQLV SIPSLFSTQH QSQQTPSFSM SATALLQKAA  360
QIGATSTDTS FLGSFGTKCS NSQIQDGSQY GDLYVSNTQT TTLGRDMENS ANDISTLNQL  420
QMYPPKRRYL QNEESGGGQT RDFLGVGVQQ AICHPSSING WI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-36	130	196	3	69	Zinc finger protein JACKDAW
5b3h_F	2e-36	130	196	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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00125	DAP	Transfer from AT1G03840	Download

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}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012479657.1	0.0	PREDICTED: zinc finger protein NUTCRACKER-like
Swissprot	Q9ZWA6	1e-156	IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBL	A0A0D2PW72	0.0	A0A0D2PW72_GOSRA; Uncharacterized protein
STRING	Gorai.005G198900.1	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-159	C2H2 family protein

Link Out ? help Back to Top
Phytozome	Gorai.005G198900.1
Entrez Gene	105794844

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] 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]