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

Glyma.19G180400.2.p

Common Name

GLYMA_19G180400, LOC100789331

Organism

Glycine max

Taxonomic ID

3847

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja

Family

C2H2

Protein Properties

Length: 469aa MW: 50961.8 Da PI: 9.1481

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.19G180400.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.3	2.8e-05	67	89	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Glyma.19G180400.2.p 67 FICEICNKGFQRDQNLQLHRRGH 89 89*******************88 PP
2	zf-C2H2	14	0.00014	143	165	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Glyma.19G180400.2.p 143 WKCEKCSKKYAVQSDWKAHTKTC 165 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.2E-5	66	89	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.48E-7	66	89	No hit	No description
PROSITE profile	PS50157	10.845	67	89	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.022	67	89	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	5.5E-5	67	89	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	69	89	IPR007087	Zinc finger, C2H2
SMART	SM00355	98	108	138	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.1E-5	131	164	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.48E-7	138	163	No hit	No description
SMART	SM00355	130	143	163	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: 469 aa Download sequence Send to blast
MQMIPGDPFS LSTSLPGLPN NEQNTNTNPN PNTPPPNKKK RNLPGTPDPD AEVIALSPKT 60 LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN KDIRKKVYIC PEKTCVHHDA 120 ARALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA HTKTCGTREY KCDCGTLFSR 180 KDSFITHRAF CDALAEESSR LTSVASTSLN FMSEDTTMMN TQASLSSSGL INGQGMQSVS 240 HFGPHGLRLM SMGTDQQRPN LSLWLNQGNH HINNPLDVAS SSSSGLPEGE GGASDLASMY 300 SESQNKNSNS ATPMSATALL QKAAQMGSTR STNPSIFSGS FGVMSSSSTQ STSLNSNSNQ 360 SSDQLNHAFQ NFNATSSSAT LLGSSTNFSS LTHSSNGFDQ FLMENNVEPT QLKLHPGSNI 420 MEQHNLTRDF LGVSGNGGGH HAFLPQELAK FASLGSSMGL NQFTAGHQ*

Sequence ? help Back to Top

Protein Sequence Length: 469 aa Download sequence Send to blast

MQMIPGDPFS LSTSLPGLPN NEQNTNTNPN PNTPPPNKKK RNLPGTPDPD AEVIALSPKT  60
LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN KDIRKKVYIC PEKTCVHHDA  120
ARALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA HTKTCGTREY KCDCGTLFSR  180
KDSFITHRAF CDALAEESSR LTSVASTSLN FMSEDTTMMN TQASLSSSGL INGQGMQSVS  240
HFGPHGLRLM SMGTDQQRPN LSLWLNQGNH HINNPLDVAS SSSSGLPEGE GGASDLASMY  300
SESQNKNSNS ATPMSATALL QKAAQMGSTR STNPSIFSGS FGVMSSSSTQ STSLNSNSNQ  360
SSDQLNHAFQ NFNATSSSAT LLGSSTNFSS LTHSSNGFDQ FLMENNVEPT QLKLHPGSNI  420
MEQHNLTRDF LGVSGNGGGH HAFLPQELAK FASLGSSMGL NQFTAGHQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	5e-38	139	205	3	69	Zinc finger protein JACKDAW
5b3h_F	5e-38	139	205	3	69	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	93	105	KLRQRSNKDIRKK

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.19G180400.2.p

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

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP015037	1e-157	AP015037.1 Vigna angularis var. angularis DNA, chromosome 4, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006604570.1	0.0	zinc finger protein JACKDAW isoform X2
Refseq	XP_028217224.1	0.0	zinc finger protein JACKDAW-like isoform X2
Swissprot	Q700D2	1e-136	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	K7MZ06	0.0	K7MZ06_SOYBN; Uncharacterized protein
STRING	GLYMA19G36430.2	0.0	(Glycine max)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	1e-101	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	Glyma.19G180400.2.p
Entrez Gene	100789331

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]