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_A04G0633

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: 433aa MW: 47614.7 Da PI: 9.5201

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A04G0633	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	16.4	2.5e-05	30	52	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Gh_A04G0633 30 FICEICNKGFQRDQNLQLHRRGH 52 89*******************88 PP
2	zf-C2H2	13	0.00031	107	129	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Gh_A04G0633 107 WKCEKCSKKYAVQSDWKAHSKTC 129 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	3.02E-7	29	52	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.1E-5	29	52	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.022	30	52	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.845	30	52	IPR007087	Zinc finger, C2H2
Pfam	PF12171	5.0E-5	30	52	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	32	52	IPR007087	Zinc finger, C2H2
SMART	SM00355	100	72	102	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.0E-4	95	128	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.02E-7	102	127	No hit	No description
SMART	SM00355	140	107	127	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: 433 aa Download sequence Send to blast
MADETDFKDM DPDAEVIALS PKTLMATNRF ICEICNKGFQ RDQNLQLHRR GHNLPWKLKQ 60 RNNKEPVKKK VYICPEKTCV HHDPSRALGD LTGIKKHFSR KHGEKKWKCE KCSKKYAVQS 120 DWKAHSKTCG TREYKCDCGT LFSRKDSFIT HRAFCDALAE ESARFSSVAG AATNLNFRND 180 VVNLPIGFGG IPQFGSGFTQ DVSGMTVSGL PEMVQMASGN LFGSSSLNNF GTDSNPPLLP 240 LPQGLNEEGG SKGKLMESLS PLYSDTQNEQ SKPAAPMSAT ALLQKAAQMG STRSKPTSFF 300 GNSFCVRSST SSQRSASLRS TQNRNDQLQQ IYPNVKQQES YLMASSSVSM SAYAGLGTSN 360 NFDRLILQTG VKQNAPNQLK MHPGSNSIDQ SLTRDFLGMG NDQSARPFLP QELAKFVSIG 420 STMGLNQFSS SNH

Sequence ? help Back to Top

Protein Sequence Length: 433 aa Download sequence Send to blast

MADETDFKDM DPDAEVIALS PKTLMATNRF ICEICNKGFQ RDQNLQLHRR GHNLPWKLKQ  60
RNNKEPVKKK VYICPEKTCV HHDPSRALGD LTGIKKHFSR KHGEKKWKCE KCSKKYAVQS  120
DWKAHSKTCG TREYKCDCGT LFSRKDSFIT HRAFCDALAE ESARFSSVAG AATNLNFRND  180
VVNLPIGFGG IPQFGSGFTQ DVSGMTVSGL PEMVQMASGN LFGSSSLNNF GTDSNPPLLP  240
LPQGLNEEGG SKGKLMESLS PLYSDTQNEQ SKPAAPMSAT ALLQKAAQMG STRSKPTSFF  300
GNSFCVRSST SSQRSASLRS TQNRNDQLQQ IYPNVKQQES YLMASSSVSM SAYAGLGTSN  360
NFDRLILQTG VKQNAPNQLK MHPGSNSIDQ SLTRDFLGMG NDQSARPFLP QELAKFVSIG  420
STMGLNQFSS SNH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-38	103	169	3	69	Zinc finger protein JACKDAW
5b3h_F	2e-38	103	169	3	69	Zinc finger protein JACKDAW
Search in ModeBase

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_017615263.1	0.0	PREDICTED: zinc finger protein JACKDAW-like isoform X1
Swissprot	Q700D2	1e-136	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A0D2V173	0.0	A0A0D2V173_GOSRA; Uncharacterized protein
STRING	Gorai.009G418600.1	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-116	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]