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

Sobic.003G034400.1.p

Organism

Sorghum bicolor

Taxonomic ID

4558

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum

Family

C3H

Protein Properties

Length: 380aa MW: 40639.4 Da PI: 7.1655

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.003G034400.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	25.3	2.6e-08	117	137	5	26
--SGGGGTS--TTTTT-SS-SS CS zf-CCCH 5 lCrffartGtCkyGdrCkFaHg 26 C++f++ G Ck+Gd+C FaHg Sobic.003G034400.1.p 117 ACPDFRK-GGCKRGDNCDFAHG 137 7****.***********9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF90229	4.87E-5	111	141	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	3.5E-5	112	138	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.46	113	139	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.8E-6	116	139	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	5.2E-6	117	137	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	12	147	170	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	6.258	147	171	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009867	Biological Process	jasmonic acid mediated signaling pathway
GO:0010150	Biological Process	leaf senescence
GO:0005634	Cellular Component	nucleus
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 380 aa Download sequence Send to blast
MMMMGEGVSV PPWTHHVPVS GVDVGGGDEM TPYLLAALRQ YLPCNDAAAG AEADDEDAAA 60 MAAGVDGYGC DEFRMYEFKV RRCARARSHD WTECPFAHPG EKARRRDPRK YHYSGTACPD 120 FRKGGCKRGD NCDFAHGVFE CWLHPARYRT QPCKDGTACR RRVCFFAHTP DQLRVLPTTQ 180 HQQSSPRGAA ACSPLADSYD GSPLRRQAVE SFRTKSIMSS SPTSTLMSPP KSPPSESPPL 240 SPDGAAAFRR GSWPGVGSPV NDVLATLRQL RLSKANSSPS GGWGGYPASA VGYASPTAGG 300 FYSLPTTPTT LATASGYMAN MEPLDVSFCG DEEPVERVES GRALRTKVFE RLSRDGAVSG 360 DATAGISGPD VGWVSDLIN*

Sequence ? help Back to Top

Protein Sequence Length: 380 aa Download sequence Send to blast

MMMMGEGVSV PPWTHHVPVS GVDVGGGDEM TPYLLAALRQ YLPCNDAAAG AEADDEDAAA  60
MAAGVDGYGC DEFRMYEFKV RRCARARSHD WTECPFAHPG EKARRRDPRK YHYSGTACPD  120
FRKGGCKRGD NCDFAHGVFE CWLHPARYRT QPCKDGTACR RRVCFFAHTP DQLRVLPTTQ  180
HQQSSPRGAA ACSPLADSYD GSPLRRQAVE SFRTKSIMSS SPTSTLMSPP KSPPSESPPL  240
SPDGAAAFRR GSWPGVGSPV NDVLATLRQL RLSKANSSPS GGWGGYPASA VGYASPTAGG  300
FYSLPTTPTT LATASGYMAN MEPLDVSFCG DEEPVERVES GRALRTKVFE RLSRDGAVSG  360
DATAGISGPD VGWVSDLIN*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Sbi.14538	0.0	callus\| embryo\| root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in leaf and panicles, but is down-regulated during natural leaf senescence, panicle development and pollination. {ECO:0000269\|PubMed:16778011}.

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in leaf senescence delay. May repress jasmonic acid (JA) signaling role in promoting leaf senescence. May regulate panicle development and pollination/fertilization process. {ECO:0000269\|PubMed:16778011}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.003G034400.1.p

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	BT085217	0.0	BT085217.2 Zea mays full-length cDNA clone ZM_BFb0336L11 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002455022.2	0.0	zinc finger CCCH domain-containing protein 2
Swissprot	Q9FU27	0.0	C3H2_ORYSJ; Zinc finger CCCH domain-containing protein 2
TrEMBL	A0A1B6Q149	0.0	A0A1B6Q149_SORBI; Uncharacterized protein
STRING	Sb03g003110.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1578	34	93
Representative plant	OGRP1170	16	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G19810.1	2e-86	C3H family protein

Link Out ? help Back to Top
Phytozome	Sobic.003G034400.1.p

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Mebel AM,Kislov VV,Hayashi M Prediction of product branching ratios in the C(3P)+C2H2-->l-C3H+H/c-C3H+H/C3+H2 reaction using ab initio coupled clusters calculations extrapolated to the complete basis set combined with Rice-Ramsperger-Kassel-Marcus and radiationless transition theories. J Chem Phys, 2007. 126(20): p. 204310 [PMID:17552765] Miyazawa T,Shibata A,Nakagawa K,Tsuzuki T Anti-angiogenic function of tocotrienol. Asia Pac J Clin Nutr, 2008. 17 Suppl 1: p. 253-6 [PMID:18296349]