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_A09G1411

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: 450aa MW: 48677.7 Da PI: 9.879

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A09G1411	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	15.5	5e-05	62	84	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Gh_A09G1411 62 FICEICKKGFQRDQNLQLHRRGH 84 89*******************88 PP
2	zf-C2H2	12.9	0.00033	138	160	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Gh_A09G1411 138 WKCEKCSKKYAVQSDWKAHSKTC 160 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	6.9E-5	61	84	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	9.89E-7	61	84	No hit	No description
SMART	SM00355	0.05	62	84	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.533	62	84	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	64	84	IPR007087	Zinc finger, C2H2
SMART	SM00355	100	103	133	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.1E-4	126	159	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	9.89E-7	133	158	No hit	No description
SMART	SM00355	140	138	158	IPR015880	Zinc finger, C2H2-like

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: 450 aa Download sequence Send to blast
MSDEAFPAAS IGGFIQDPSN ANPNPKPNAN PAKKKRNLPG TPDPDAEVIA LSPKTLMATN 60 RFICEICKKG FQRDQNLQLH RRGHNLPWKL RQRTNKEVRK KVYICPEKTC VHHDPSRALG 120 DLTGIKKHFS RKHGEKKWKC EKCSKKYAVQ SDWKAHSKTC GTREYKCDCG TLFSRKDSFI 180 THRAFCDALA EESARLTSVA ATSLNFRNDT VNLPHGFASR GVQDVAGIPQ FGSGFPQDFS 240 GMPAPGLSEM VQMAPANLFG SSSHFPGFEN GGATSSNSNN LSLSQLPQGL KEEGGNEGNL 300 MESLSSLYSD NQNKQSKANA SPMSATALLQ KAAQMGSTRS SPSFFGNSFG VMSSSSSHTA 360 PTFMASSSAS MSAKSNNLDK LMLQTGGKPS EPSLLSMHHP GSNSFAQSLT RDFLGMSNDQ 420 SPRPFLPQEL AKYAAIGSSI GLSQFTSSNH

Sequence ? help Back to Top

Protein Sequence Length: 450 aa Download sequence Send to blast

MSDEAFPAAS IGGFIQDPSN ANPNPKPNAN PAKKKRNLPG TPDPDAEVIA LSPKTLMATN  60
RFICEICKKG FQRDQNLQLH RRGHNLPWKL RQRTNKEVRK KVYICPEKTC VHHDPSRALG  120
DLTGIKKHFS RKHGEKKWKC EKCSKKYAVQ SDWKAHSKTC GTREYKCDCG TLFSRKDSFI  180
THRAFCDALA EESARLTSVA ATSLNFRNDT VNLPHGFASR GVQDVAGIPQ FGSGFPQDFS  240
GMPAPGLSEM VQMAPANLFG SSSHFPGFEN GGATSSNSNN LSLSQLPQGL KEEGGNEGNL  300
MESLSSLYSD NQNKQSKANA SPMSATALLQ KAAQMGSTRS SPSFFGNSFG VMSSSSSHTA  360
PTFMASSSAS MSAKSNNLDK LMLQTGGKPS EPSLLSMHHP GSNSFAQSLT RDFLGMSNDQ  420
SPRPFLPQEL AKYAAIGSSI GLSQFTSSNH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-38	134	200	3	69	Zinc finger protein JACKDAW
5b3h_F	1e-38	134	200	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	88	100	KLRQRTNKEVRKK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Ghi.10937	0.0	boll\| root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269\|PubMed:17785527}.
Uniprot	TISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269\|PubMed:17785527}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:20356954, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:28211915}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by SCR and SHR. {ECO:0000269\|PubMed:21935722}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016669586.1	0.0	PREDICTED: zinc finger protein JACKDAW-like
Swissprot	Q700D2	1e-129	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A1U8HUB1	0.0	A0A1U8HUB1_GOSHI; zinc finger protein JACKDAW-like
STRING	Gorai.006G167600.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM155	28	306

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	1e-128	C2H2-like zinc finger protein

Publications ? help Back to Top
Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]