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.007G000400.1.p

Common Name

Sb07g000220, SORBIDRAFT_07g000220

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

Protein Properties

Length: 372aa MW: 40080.8 Da PI: 6.5899

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.007G000400.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	41.5	2.4e-13	266	351	3	84
EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS B3 3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkl 84 k+lt+sdv +sgr+vlpkk ae+ +++ + l++ d W++k+++ ++ks++y+l+ eFvk +gL++gD ++++ Sobic.007G000400.1.p 266 KELTKSDVANSGRIVLPKKDAEAGlpPLVQGDPLILQMDDmVLPIIWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDALIIYK 351 899****************88899666666656676664445***99888888888888.99**************993 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.57E-14	263	353	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	6.9E-20	263	367	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.54E-19	263	361	No hit	No description
SMART	SM01019	7.6E-8	264	364	IPR003340	B3 DNA binding domain
Pfam	PF02362	8.6E-10	266	352	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 372 aa Download sequence Send to blast
MGQMGGPDGD GDGGGGGPHH QYHYQALLAA VQNPSQGLHP FPLPFHLPLH AGAPAAGPVV 60 ADADAASTHG ANANAAPHSQ PPRGFTDWSP SNSAFAAVAA QPAPATTNTP FHYNVPQSYA 120 LWTHYMLNKN VSCSTYPTQH EENPHPLRQT HIPEENPHPL RHSHIPDKDS GCASSLGFDS 180 FTTMSLGPNI CAHMTPMEGS ISAKEPENSQ DLPAVVRSSD EMDTRNSGEV HRDTAGTLPE 240 SKQSHESCAS MSNKFNSGEY QVILRKELTK SDVANSGRIV LPKKDAEAGL PPLVQGDPLI 300 LQMDDMVLPI IWKFKYRFWP NNKSRMYILE AAGEFVKTHG LQAGDALIIY KNSVPGKFII 360 RGEKSIQQTN P*

Sequence ? help Back to Top

Protein Sequence Length: 372 aa Download sequence Send to blast

MGQMGGPDGD GDGGGGGPHH QYHYQALLAA VQNPSQGLHP FPLPFHLPLH AGAPAAGPVV  60
ADADAASTHG ANANAAPHSQ PPRGFTDWSP SNSAFAAVAA QPAPATTNTP FHYNVPQSYA  120
LWTHYMLNKN VSCSTYPTQH EENPHPLRQT HIPEENPHPL RHSHIPDKDS GCASSLGFDS  180
FTTMSLGPNI CAHMTPMEGS ISAKEPENSQ DLPAVVRSSD EMDTRNSGEV HRDTAGTLPE  240
SKQSHESCAS MSNKFNSGEY QVILRKELTK SDVANSGRIV LPKKDAEAGL PPLVQGDPLI  300
LQMDDMVLPI IWKFKYRFWP NNKSRMYILE AAGEFVKTHG LQAGDALIIY KNSVPGKFII  360
RGEKSIQQTN P*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9c_A	3e-29	255	352	4	101	B3 domain-containing transcription factor LEC2
6j9c_D	3e-29	255	352	4	101	B3 domain-containing transcription factor LEC2
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Sbi.14098	0.0	ovary

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots. {ECO:0000269\|PubMed:18025467}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription regulator involved in iron deficiency response and tolerance. May regulate directly iron transporters or other transcription factors involved in iron-deficiency response. Binds specifically to the DNA sequence 5'-CATGC-3' of the IDE1 element found in the promoter of the barley iron deficiency-inducible gene IDS2. {ECO:0000269\|PubMed:18025467}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.007G000400.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated during the early stage of iron deficiency (at protein level). {ECO:0000269\|PubMed:27137867}.

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	BT038952	0.0	BT038952.1 Zea mays full-length cDNA clone ZM_BFb0345D11 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021321516.1	0.0	B3 domain-containing protein IDEF1 isoform X1
Swissprot	Q6Z1Z3	1e-118	IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBL	C5YLC1	0.0	C5YLC1_SORBI; Uncharacterized protein
STRING	Sb07g000220.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP11346	28	31
Representative plant	OGRP788	17	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24650.1	4e-32	B3 family protein

Link Out ? help Back to Top
Phytozome	Sobic.007G000400.1.p
Entrez Gene	8064312

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] Kobayashi T, et al. The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes. Plant J., 2009. 60(6): p. 948-61 [PMID:19737364] Kobayashi T, et al. The spatial expression and regulation of transcription factors IDEF1 and IDEF2. Ann. Bot., 2010. 105(7): p. 1109-17 [PMID:20197292] Kobayashi T, et al. The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status. Plant J., 2012. 69(1): p. 81-91 [PMID:21880076] Itai RN,Ogo Y,Kobayashi T,Nakanishi H,Nishizawa NK Rice genes involved in phytosiderophore biosynthesis are synchronously regulated during the early stages of iron deficiency in roots. Rice (N Y), 2013. 6(1): p. 16 [PMID:24280375] Kobayashi T,Nishizawa NK Iron sensors and signals in response to iron deficiency. Plant Sci., 2014. 224: p. 36-43 [PMID:24908504] Kobayashi T,Nakanishi Itai R,Nishizawa NK Iron deficiency responses in rice roots. Rice (N Y), 2014. 7(1): p. 27 [PMID:26224556] Tan S, et al. CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa. Sci Rep, 2016. 6: p. 25485 [PMID:27137867] Kobayashi T, et al. Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots. Plant Mol. Biol., 2016. 91(4-5): p. 533-47 [PMID:27143046]