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.001G526800.2.p

Common Name

Sb01g049020, SORBIDRAFT_01g049020

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: 234aa MW: 26411.4 Da PI: 9.3413

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.001G526800.2.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	92.3	2.3e-29	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+++fs++gkl+e++s Sobic.001G526800.2.p 9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALVVFSPRGKLFEFAS 59 79***********************************************86 PP
2	K-box	68	3.1e-23	78	171	6	99
K-box 6 gksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaL 94 ++++ +++ e+ + +++ L k++e L +R+llGe Le++s++eL++Le +Leksl iR +K+ ll eq+++l++ke +l++ n++L Sobic.001G526800.2.p 78 SNKTVQQDIEQVKADAEGLAKKLEALDAYKRKLLGERLEECSIEELHSLEVKLEKSLHCIRGRKTLLLEEQVNKLKEKEMNLRKSNEDL 166 33467788999**************************************************************************** PP K-box 95 rkkle 99 r+k + Sobic.001G526800.2.p 167 REKCK 171 976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	8.5E-40	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	31.132	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.09E-32	3	84	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.23E-41	3	78	No hit	No description
PRINTS	PR00404	1.1E-30	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.1E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-30	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-30	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	2.6E-23	83	171	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	13.076	86	176	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000060	Biological Process	protein import into nucleus, translocation
GO:0009409	Biological Process	response to cold
GO:0009739	Biological Process	response to gibberellin
GO:0009911	Biological Process	positive regulation of flower development
GO:0010077	Biological Process	maintenance of inflorescence meristem identity
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0005737	Cellular Component	cytoplasm
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0008134	Molecular Function	transcription factor binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 234 aa Download sequence Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALVVFSP RGKLFEFASG 60 SVQKTIERYR TYTKDNASNK TVQQDIEQVK ADAEGLAKKL EALDAYKRKL LGERLEECSI 120 EELHSLEVKL EKSLHCIRGR KTLLLEEQVN KLKEKEMNLR KSNEDLREKC KKQPPMLMAP 180 PPPPVPAVMT VEDDHPEPKD DGVDVETELY IGLPGRDYRS NKDKAAVAVS RSG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	1e-19	1	72	1	72	MEF2C
5f28_B	1e-19	1	72	1	72	MEF2C
5f28_C	1e-19	1	72	1	72	MEF2C
5f28_D	1e-19	1	72	1	72	MEF2C
6byy_A	1e-19	1	78	1	78	MEF2 CHIMERA
6byy_B	1e-19	1	78	1	78	MEF2 CHIMERA
6byy_C	1e-19	1	78	1	78	MEF2 CHIMERA
6byy_D	1e-19	1	78	1	78	MEF2 CHIMERA
6bz1_A	2e-19	1	78	1	78	MEF2 CHIMERA
6bz1_B	2e-19	1	78	1	78	MEF2 CHIMERA
6bz1_C	2e-19	1	78	1	78	MEF2 CHIMERA
6bz1_D	2e-19	1	78	1	78	MEF2 CHIMERA
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Low expression in the young panicle continues to decline as the organ mature. {ECO:0000269\|PubMed:15144377, ECO:0000269\|PubMed:17166135}.
Uniprot	TISSUE SPECIFICITY: Expressed in mature leaves and at low levels in roots and young panicles. {ECO:0000269\|PubMed:15144377, ECO:0000269\|PubMed:17166135}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor active in flowering time control. May control internode elongation and promote floral transition phase. May act upstream of the floral regulators MADS1, MADS14, MADS15 and MADS18 in the floral induction pathway. {ECO:0000269\|PubMed:15144377, ECO:0000269\|PubMed:17166135}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00076	ChIP-chip	Transfer from AT2G45660	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.001G526800.2.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	AJ430642	0.0	AJ430642.1 Zea mays mRNA for putative MADS-domain transcription factor (m5 gene).
GenBank	BT055216	0.0	BT055216.1 Zea mays full-length cDNA clone ZM_BFc0137M15 mRNA, complete cds.
GenBank	HQ858775	0.0	HQ858775.1 Zea mays clone UT1761 MADS transcription factor mRNA, partial cds.
GenBank	KM101125	0.0	KM101125.1 Zea mays cultivar 18-599 SOC1 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002465961.1	1e-171	MADS-box transcription factor 50
Refseq	XP_021307505.1	1e-171	MADS-box transcription factor 50
Swissprot	Q9XJ60	1e-116	MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBL	A0A1Z5SBR0	1e-169	A0A1Z5SBR0_SORBI; Uncharacterized protein
STRING	Sb01g049020.1	1e-170	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP1413	33	79
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45660.1	2e-71	AGAMOUS-like 20

Link Out ? help Back to Top
Phytozome	Sobic.001G526800.2.p
Entrez Gene	8077968

Publications ? help Back to Top
Thomson MJ,Edwards JD,Septiningsih EM,Harrington SE,McCouch SR Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics, 2006. 172(4): p. 2501-14 [PMID:16452146] Park SJ, et al. Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod. Plant J., 2008. 56(6): p. 1018-29 [PMID:18774969] Lee S,Jeong DH,An G A possible working mechanism for rice SVP-group MADS-box proteins as negative regulators of brassinosteroid responses. Plant Signal Behav, 2008. 3(7): p. 471-4 [PMID:19704489] Maas LF,McClung A,McCouch S Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. Theor. Appl. Genet., 2010. 120(5): p. 895-908 [PMID:19949767] Sun C, et al. The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice. Plant Cell, 2012. 24(8): p. 3235-47 [PMID:22892321] Choi SC, et al. Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3. Plant Physiol., 2014. 164(3): p. 1326-37 [PMID:24420930] Núñez-López L,Aguirre-Cruz A,Barrera-Figueroa BE,Peña-Castro JM Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor. PeerJ, 2015. 3: p. e817 [PMID:25780769] Jin J, et al. MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice. Plant Physiol., 2015. 168(4): p. 1275-85 [PMID:25855537] Liu X, et al. Brassinosteroid (BR) biosynthetic gene lhdd10 controls late heading and plant height in rice (Oryza sativa L.). Plant Cell Rep., 2016. 35(2): p. 357-68 [PMID:26518431] Hwang YH, et al. Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time. Plant Cell Rep., 2016. 35(4): p. 857-65 [PMID:26754793] Shibaya T, et al. Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice. Plant Cell Physiol., 2016. 57(9): p. 1828-38 [PMID:27318280] Alter P, et al. Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1. Plant Physiol., 2016. 172(1): p. 389-404 [PMID:27457125]