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.002G343300.1.p

Common Name

Sb02g036710, SORBIDRAFT_02g036710

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: 681aa MW: 72441.2 Da PI: 7.3245

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.002G343300.1.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	24.8	3.7e-08	285	307	4	26
---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 4 elCrffartGtCkyGdrCkFaHg 26 ++C++f+r G C+ Gd+C F+Hg Sobic.002G343300.1.p 285 VPCPNFRRPGGCPSGDSCEFSHG 307 79********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF48403	1.17E-14	74	154	IPR020683	Ankyrin repeat-containing domain
Gene3D	G3DSA:1.25.40.20	2.4E-16	75	155	IPR020683	Ankyrin repeat-containing domain
SMART	SM00248	0.18	76	106	IPR002110	Ankyrin repeat
PROSITE profile	PS50088	8.923	76	100	IPR002110	Ankyrin repeat
PROSITE profile	PS50297	17.661	76	151	IPR020683	Ankyrin repeat-containing domain
Pfam	PF12796	1.0E-9	76	143	IPR020683	Ankyrin repeat-containing domain
CDD	cd00204	1.00E-13	78	154	No hit	No description
SMART	SM00248	0.0032	111	143	IPR002110	Ankyrin repeat
PROSITE profile	PS50088	12.903	111	146	IPR002110	Ankyrin repeat
PRINTS	PR01415	7.8E-5	112	127	IPR002110	Ankyrin repeat
PRINTS	PR01415	7.8E-5	130	144	IPR002110	Ankyrin repeat
SMART	SM00356	5.6E-4	281	308	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.995	281	309	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.75E-5	282	310	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.7E-6	285	307	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.5E-6	285	308	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.7E-4	313	346	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	21	317	340	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0005737	Cellular Component	cytoplasm
GO:0005515	Molecular Function	protein binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 681 aa Download sequence Send to blast
MGDLADLGGA GESARSHVAA AGGGGQRDRL AALLELAAAD DAVGFREALA VGGAQGNLAE 60 LADGVGLWYG RSKAYEPRTP LMVAATYGSV EVVSLLLGLG CVDVNRRPGV DGATPLHCAA 120 SGGSRNAVAV VKLLLAAGAD PVTPDSAGRL PADVILSPPA SPDALGDLEM LLGRRRGLAV 180 ATSVPSRSSS PPLSSSPDEG NRSPSSRSSS LSPITVDRAK KEYPVDPTLP DIKSSVYASD 240 EFRMFAFKVR PCSRAYSHDW TECPFVHPGE NARRRDPRKH PYTAVPCPNF RRPGGCPSGD 300 SCEFSHGVFE SWLHPSQYRT RLCKEGAACA RRICFFAHDE DELRHVPHNN GAGLLSPRAS 360 SSIDMTAAAA LGLLPGSPTR HFVPPPLSPS AANNGGGAAA AHWLQGSRLR SSFNARDAQV 420 DDLGALLEWE SQYLGALSLP QSSRSQPRLS TGLSIRPTGI APSNLEEMYA SDMAMSPRFT 480 NDQGHSVYSP AHKSALLNKF HHQQKGLLSP VNTNRMYSPR GLDPSILHYP YGGMSPRSPR 540 TMEPTSPLSV CVGATVTQRD MLDQFSSLNK HQVPSVGSPR NLNASWGNIG TPKSKVDWGV 600 DDDELVRLRH PVQPGNTAEE PDVSWVQSLV NHAELNGKRG EMAGMASRSI NRPDLSSQGD 660 SLDQSVIASW LEQQMHLEPK *

Sequence ? help Back to Top

Protein Sequence Length: 681 aa Download sequence Send to blast

MGDLADLGGA GESARSHVAA AGGGGQRDRL AALLELAAAD DAVGFREALA VGGAQGNLAE  60
LADGVGLWYG RSKAYEPRTP LMVAATYGSV EVVSLLLGLG CVDVNRRPGV DGATPLHCAA  120
SGGSRNAVAV VKLLLAAGAD PVTPDSAGRL PADVILSPPA SPDALGDLEM LLGRRRGLAV  180
ATSVPSRSSS PPLSSSPDEG NRSPSSRSSS LSPITVDRAK KEYPVDPTLP DIKSSVYASD  240
EFRMFAFKVR PCSRAYSHDW TECPFVHPGE NARRRDPRKH PYTAVPCPNF RRPGGCPSGD  300
SCEFSHGVFE SWLHPSQYRT RLCKEGAACA RRICFFAHDE DELRHVPHNN GAGLLSPRAS  360
SSIDMTAAAA LGLLPGSPTR HFVPPPLSPS AANNGGGAAA AHWLQGSRLR SSFNARDAQV  420
DDLGALLEWE SQYLGALSLP QSSRSQPRLS TGLSIRPTGI APSNLEEMYA SDMAMSPRFT  480
NDQGHSVYSP AHKSALLNKF HHQQKGLLSP VNTNRMYSPR GLDPSILHYP YGGMSPRSPR  540
TMEPTSPLSV CVGATVTQRD MLDQFSSLNK HQVPSVGSPR NLNASWGNIG TPKSKVDWGV  600
DDDELVRLRH PVQPGNTAEE PDVSWVQSLV NHAELNGKRG EMAGMASRSI NRPDLSSQGD  660
SLDQSVIASW LEQQMHLEPK *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5elk_A	5e-11	247	340	14	118	RING finger protein unkempt homolog
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.002G343300.1.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	BT054366	0.0	BT054366.1 Zea mays full-length cDNA clone ZM_BFc0002O06 mRNA, complete cds.
GenBank	BT054447	0.0	BT054447.1 Zea mays full-length cDNA clone ZM_BFc0063F04 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002460875.1	0.0	zinc finger CCCH domain-containing protein 50
Swissprot	Q84SL2	0.0	C3H50_ORYSJ; Zinc finger CCCH domain-containing protein 50
TrEMBL	C5XBP2	0.0	C5XBP2_SORBI; Uncharacterized protein
STRING	Sb02g036710.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP823	37	126
Representative plant	OGRP709	15	69

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G12850.1	1e-129	CCCH-type zinc finger protein with ARM repeat domain

Link Out ? help Back to Top
Phytozome	Sobic.002G343300.1.p
Entrez Gene	8056356

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]