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.010G261800.1.p

Common Name

Sb10g029810, SORBIDRAFT_10g029810

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

MIKC_MADS

Protein Properties

Length: 227aa MW: 25722.1 Da PI: 9.2125

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.010G261800.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	90.5	8.4e-29	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien +nrqvt+skRr+gi+KKA EL vLCda+va+i+fsstgk +e++s Sobic.010G261800.1.p 9 KRIENATNRQVTYSKRRTGIMKKARELTVLCDAQVAIIMFSSTGKYHEFCS 59 79***********************************************96 PP
2	K-box	87	3.7e-29	71	168	1	98
K-box 1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqe 89 yq++ g+sl+++++e++q+ l+ Lk+ ++nL++e+R+++GedL++L++ eL+ Leq+++ +lk++R +K++++ +q+e+ +kk k e Sobic.010G261800.1.p 71 YQQAIGTSLWNEQYENMQRTLSHLKDINRNLRTEIRQRMGEDLDTLEFDELRGLEQNVDAALKEVRHRKYHVIATQTETYKKKVKHSYE 159 67888999******************************************************************************* PP K-box 90 enkaLrkkl 98 + k+L+++l Sobic.010G261800.1.p 160 AYKNLQQEL 168 ****986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	2.6E-42	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	32.59	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.57E-36	2	95	IPR002100	Transcription factor, MADS-box
CDD	cd00265	9.27E-43	2	80	No hit	No description
PRINTS	PR00404	2.3E-28	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.0E-24	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.3E-28	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.3E-28	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	1.9E-21	82	168	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.081	84	174	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010093	Biological Process	specification of floral organ identity
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 227 aa Download sequence Send to blast
MGRGKIEIKR IENATNRQVT YSKRRTGIMK KARELTVLCD AQVAIIMFSS TGKYHEFCSP 60 GTDIKTIFDR YQQAIGTSLW NEQYENMQRT LSHLKDINRN LRTEIRQRMG EDLDTLEFDE 120 LRGLEQNVDA ALKEVRHRKY HVIATQTETY KKKVKHSYEA YKNLQQELGM REDPAFGFVD 180 NTGAGGWDGA AAALGGGAPD MYAFRVVPSQ PNLHGMAYGS HDLRLG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	7e-18	1	86	1	78	MEF2C
5f28_B	7e-18	1	86	1	78	MEF2C
5f28_C	7e-18	1	86	1	78	MEF2C
5f28_D	7e-18	1	86	1	78	MEF2C
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in lodicules, stamens and carpels. {ECO:0000269\|PubMed:10394955, ECO:0000269\|PubMed:12506001, ECO:0000269\|PubMed:12905025, ECO:0000269\|PubMed:14558657}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the development of floral organs. Required for normal development of lodicules and stamens (whorls 2 and 3). May function as a heterodimer with MADS4. {ECO:0000269\|PubMed:12506001, ECO:0000269\|PubMed:12905025, ECO:0000269\|PubMed:14558657}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00077	ChIP-seq	Transfer from AT3G54340	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.010G261800.1.p

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT039988	0.0	BT039988.1 Zea mays full-length cDNA clone ZM_BFc0056L03 mRNA, complete cds.
GenBank	EU966237	0.0	EU966237.1 Zea mays clone 292756 MADS-box transcription factor 16 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002439003.1	1e-171	MADS-box transcription factor 16
Swissprot	Q944S9	1e-142	MAD16_ORYSJ; MADS-box transcription factor 16
TrEMBL	C5Z1S2	1e-170	C5Z1S2_SORBI; Uncharacterized protein
STRING	Sb10g029810.1	1e-171	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP5728	35	52
Representative plant	OGRP5199	11	21

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54340.1	3e-65	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Sobic.010G261800.1.p
Entrez Gene	8064983

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] Chen ZX, et al. Morphogenesis and molecular basis on naked seed rice, a novel homeotic mutation of OsMADS1 regulating transcript level of AP3 homologue in rice. Planta, 2006. 223(5): p. 882-90 [PMID:16254725] Zhang Q, et al. Morphological, anatomical and genetic analysis for a rice mutant with abnormal hull. J Genet Genomics, 2007. 34(6): p. 519-26 [PMID:17601611] Yoshida H, et al. superwoman1-cleistogamy, a hopeful allele for gene containment in GM rice. Plant Biotechnol. J., 2007. 5(6): p. 835-46 [PMID:17764519] Yao SG,Ohmori S,Kimizu M,Yoshida H Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development. Plant Cell Physiol., 2008. 49(5): p. 853-7 [PMID:18378529] Xiao H, et al. STAMENLESS 1, encoding a single C2H2 zinc finger protein, regulates floral organ identity in rice. Plant J., 2009. 59(5): p. 789-801 [PMID:19453444] Seok HY, et al. Rice ternary MADS protein complexes containing class B MADS heterodimer. Biochem. Biophys. Res. Commun., 2010. 401(4): p. 598-604 [PMID:20888318] Li H, et al. Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate. Plant Cell, 2011. 23(7): p. 2536-52 [PMID:21784949] Sato H,Yoshida K,Mitsuda N,Ohme-Takagi M,Takamizo T Male-sterile and cleistogamous phenotypes in tall fescue induced by chimeric repressors of SUPERWOMAN1 and OsMADS58. Plant Sci., 2012. 183: p. 183-9 [PMID:22195592] Ohmori S,Tabuchi H,Yatou O,Yoshida H Agronomic traits and gene containment capability of cleistogamous rice lines with the superwoman1-cleistogamy mutation. Breed. Sci., 2012. 62(2): p. 124-32 [PMID:23136523] Yun D, et al. OsMADS16 genetically interacts with OsMADS3 and OsMADS58 in specifying floral patterning in rice. Mol Plant, 2013. 6(3): p. 743-56 [PMID:23300256] Lombardo F, et al. The superwoman1-cleistogamy2 mutant is a novel resource for gene containment in rice. Plant Biotechnol. J., 2017. 15(1): p. 97-106 [PMID:27336225]