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.007G059500.1.p

Common Name

Sb07g004740, SORBIDRAFT_07g004740

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

NF-YB

Protein Properties

Length: 276aa MW: 27666.5 Da PI: 6.3989

Description

NF-YB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.007G059500.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YB	177.9	9.3e-56	58	153	2	97
NF-YB 2 reqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkky 90 +eqdrflPianvsrimk+ lPanakisk+aketvqecvsefisfvt+easdkcqrekrktingddllwa++tlGfe yv plk yl++y Sobic.007G059500.1.p 58 KEQDRFLPIANVSRIMKRSLPANAKISKEAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEAYVSPLKSYLNRY 146 89************************************************************************************* PP NF-YB 91 relegek 97 re+egek Sobic.007G059500.1.p 147 REAEGEK 153 **997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.20.10	6.8E-52	54	156	IPR009072	Histone-fold
SuperFamily	SSF47113	1.12E-38	60	165	IPR009072	Histone-fold
Pfam	PF00808	7.4E-27	63	127	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
PRINTS	PR00615	1.0E-18	91	109	No hit	No description
PROSITE pattern	PS00685	0	94	110	IPR003956	Transcription factor, NFYB/HAP3, conserved site
PRINTS	PR00615	1.0E-18	110	128	No hit	No description
PRINTS	PR00615	1.0E-18	129	147	No hit	No description

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:0043565	Molecular Function	sequence-specific DNA binding
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 276 aa Download sequence Send to blast
MKSRKGYGHQ GHLLSPVGSP PSDNESGAVA AAATAGGGGG CGSSVGYCGG GGGESPAKEQ 60 DRFLPIANVS RIMKRSLPAN AKISKEAKET VQECVSEFIS FVTGEASDKC QREKRKTING 120 DDLLWAMTTL GFEAYVSPLK SYLNRYREAE GEKAAVLGGA RHGDGAVDDG PLAAGGAVPP 180 SGAAGGDRAG HDGAADADAH VGLMMGGASS VVGFGAGGGA AASYYTATAA RKAYGAGEGS 240 TKVMEFEGIA GEEENGGVQR GRGFANNHLH GAVQW*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4g91_B	5e-46	58	148	2	92	Transcription factor HapC (Eurofung)
4g92_B	5e-46	58	148	2	92	Transcription factor HapC (Eurofung)
5g49_A	5e-46	52	148	1	97	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots, culms, nodes, leaf blades, leaf sheaths and young panicles. {ECO:0000269\|PubMed:20566706}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in the regulation of flowering time under long day (LD) conditions. Functions as repressor of flowering, independently of HD1 and GHD7. Controls flowering time by negatively regulating the expression of EHD1 and HD3A (PubMed:20566706, PubMed:21148627). Regulates plant height by promoting cell elongation in the internodes (PubMed:20566706). Component of the NF-Y/HAP transcription factor complex (By similarity). {ECO:0000250, ECO:0000269\|PubMed:20566706, ECO:0000269\|PubMed:21148627}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.007G059500.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Circadian-regulation under long day (LD) conditions. Expression increases in the middle of daytime, peaks around the end of the light period and gradually decreases during the dark period and beginning of daylight. {ECO:0000269\|PubMed:26542958}.

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	AB124648	1e-144	AB124648.1 Oryza sativa Indica Group Hd5 gene for Heading date 5, complete cds, cultivar:Kasalath.
GenBank	AB124649	1e-144	AB124649.1 Oryza sativa Indica Group Hd5 mRNA for Heading date 5, complete cds, cultivar:Kasalath.
GenBank	AY062182	1e-144	AY062182.1 Oryza sativa (indica cultivar-group) HAP3-like transcriptional-activator (HAP3b) mRNA, complete cds.
GenBank	CP012616	1e-144	CP012616.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 8 sequence.
GenBank	CT837794	1e-144	CT837794.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCRA121O04, full insert sequence.
GenBank	LC016712	1e-144	LC016712.1 Oryza sativa Indica Group Hd5 gene for heading date 5, complete cds, cultivar: Qiu Zhao Zong.
GenBank	LC016713	1e-144	LC016713.1 Oryza sativa Indica Group Hd5 gene for heading date 5, complete cds, cultivar: Tupa 121-3.
GenBank	LC016716	1e-144	LC016716.1 Oryza sativa Indica Group Hd5 gene for heading date 5, complete cds, cultivar: Deng Pao Zhai.
GenBank	LC016718	1e-144	LC016718.1 Oryza sativa Indica Group Hd5 gene for heading date 5, complete cds, cultivar: Naba.
GenBank	LC016719	1e-144	LC016719.1 Oryza sativa Indica Group Hd5 gene for heading date 5, complete cds, cultivar: Bei Khe.
GenBank	LC016721	1e-144	LC016721.1 Oryza sativa Indica Group Hd5 gene for heading date 5, complete cds, cultivar: Bleiyo.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002445142.1	0.0	nuclear transcription factor Y subunit B-11
Swissprot	Q0J7P4	6e-81	HD5_ORYSJ; Nuclear transcription factor Y subunit B-11
TrEMBL	C5YHV2	0.0	C5YHV2_SORBI; Uncharacterized protein
STRING	Sb07g004740.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP201	38	331
Representative plant	OGRP168	17	170

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G14540.1	4e-61	nuclear factor Y, subunit B3

Link Out ? help Back to Top
Phytozome	Sobic.007G059500.1.p
Entrez Gene	8069671

Publications ? help Back to Top
Yan WH, et al. A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant, 2011. 4(2): p. 319-30 [PMID:21148627] Dai X, et al. LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon). J Integr Plant Biol, 2012. 54(10): p. 790-9 [PMID:22963226] Kim SK, et al. OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice. Planta, 2016. 243(3): p. 563-76 [PMID:26542958]