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.13G139000.2.p

Common Name

GLYMA_13G139000, LOC100801182

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: 526aa MW: 56452 Da PI: 9.8021

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.13G139000.2.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	16.1	3.2e-05	65	87	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Glyma.13G139000.2.p 65 FICEICNKGFQRDQNLQLHRRGH 87 89*******************88 PP
2	zf-C2H2	13.9	0.00017	141	163	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Glyma.13G139000.2.p 141 WKCEKCSKKYAVQSDWKAHTKTC 163 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	1.4E-5	64	87	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.02E-7	64	87	No hit	No description
Pfam	PF12171	6.3E-5	65	87	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.022	65	87	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.845	65	87	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	67	87	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	106	136	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.6E-4	129	162	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.02E-7	136	161	No hit	No description
SMART	SM00355	130	141	161	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: 526 aa Download sequence Send to blast
MQMMPGDPFS LSTSIGGFTQ DKQNTNPNPK PNPPPKKKRN LPGTPDPDAE VIALSPKTLM 60 ATNRFICEIC NKGFQRDQNL QLHRRGHNLP WKLRQRSNKE VRKKVYICPE QTCVHHDPAR 120 ALGDLTGIKK HFSRKHGEKK WKCEKCSKKY AVQSDWKAHT KTCGTREYKC DCGTLFSRKD 180 SFITHRAFCD ALAEESARLT SVTTTNLNFK SEEGGNNVMN SQQHGLGGHG LIGAQSLQNV 240 SGIPQFGSHG FRLDFNGMEQ QIRPSLSLWL NQGNHQMNSN NNNINSNNNS ASDAGPNYMS 300 SSGLPEIVQM AHANALMGCS SSMVSNFGGV HAGSNSSSAN LSLGKRGEAC GSTVVDLASI 360 YNNSEGQNKN SKPASPMSAT ALLQKAAQMG STRSTNPSIF SGSFGVINSP SSQTTSLNNN 420 NNGGAAMMLA SNTSTAAANA NDFSSLRHSS NSFDQLVMQT NAQLQSEPVK LKLHSNGMEN 480 NLTRDFLGVS GGGGGGGGPQ FLPQELGKFA SMGSPMGLSQ FTSNQ*

Sequence ? help Back to Top

Protein Sequence Length: 526 aa Download sequence Send to blast

MQMMPGDPFS LSTSIGGFTQ DKQNTNPNPK PNPPPKKKRN LPGTPDPDAE VIALSPKTLM  60
ATNRFICEIC NKGFQRDQNL QLHRRGHNLP WKLRQRSNKE VRKKVYICPE QTCVHHDPAR  120
ALGDLTGIKK HFSRKHGEKK WKCEKCSKKY AVQSDWKAHT KTCGTREYKC DCGTLFSRKD  180
SFITHRAFCD ALAEESARLT SVTTTNLNFK SEEGGNNVMN SQQHGLGGHG LIGAQSLQNV  240
SGIPQFGSHG FRLDFNGMEQ QIRPSLSLWL NQGNHQMNSN NNNINSNNNS ASDAGPNYMS  300
SSGLPEIVQM AHANALMGCS SSMVSNFGGV HAGSNSSSAN LSLGKRGEAC GSTVVDLASI  360
YNNSEGQNKN SKPASPMSAT ALLQKAAQMG STRSTNPSIF SGSFGVINSP SSQTTSLNNN  420
NNGGAAMMLA SNTSTAAANA NDFSSLRHSS NSFDQLVMQT NAQLQSEPVK LKLHSNGMEN  480
NLTRDFLGVS GGGGGGGGPQ FLPQELGKFA SMGSPMGLSQ FTSNQ*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-37	137	206	3	72	Zinc finger protein JACKDAW
5b3h_F	1e-37	137	206	3	72	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	91	103	KLRQRSNKEVRKK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.19036	0.0	root\| somatic embryo\| vegetative bud

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.13G139000.2.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	AP015041	0.0	AP015041.1 Vigna angularis var. angularis DNA, chromosome 8, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003541407.1	0.0	zinc finger protein JACKDAW
Swissprot	Q700D2	1e-121	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	K7LZN2	0.0	K7LZN2_SOYBN; Uncharacterized protein
STRING	GLYMA13G20231.1	0.0	(Glycine max)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	1e-104	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	Glyma.13G139000.2.p
Entrez Gene	100801182

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]