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

Rsa1.0_00016.1_g00003.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

NF-YA

Protein Properties

Length: 290aa MW: 31430.7 Da PI: 6.6519

Description

NF-YA family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00016.1_g00003.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	CBFB_NFYA	94.4	1.3e-29	186	241	1	58
CBFB_NFYA 1 deplYVNaKQyqrIlkRRqkRakleeekkldeksrkpylheSRhkhAlrRpRgsgGrF 58 +ep+YVNaKQy++Il+RR++Rak+e e+k+ +rkpylheSRhkhA+rR+R+sgGrF Rsa1.0_00016.1_g00003.1 186 QEPVYVNAKQYEGILRRRKARAKAELERKV--INRKPYLHESRHKHAMRRARASGGRF 241 69*************************9..89*********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00521	4.4E-31	184	244	IPR001289	Nuclear transcription factor Y subunit A
PROSITE profile	PS51152	34.587	185	244	IPR001289	Nuclear transcription factor Y subunit A
Pfam	PF02045	4.5E-26	187	241	IPR001289	Nuclear transcription factor Y subunit A
PRINTS	PR00616	4.2E-23	188	210	IPR001289	Nuclear transcription factor Y subunit A
PROSITE pattern	PS00686	0	190	210	IPR018362	CCAAT-binding factor, conserved site
PRINTS	PR00616	4.2E-23	218	241	IPR001289	Nuclear transcription factor Y subunit A

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010262	Biological Process	somatic embryogenesis
GO:0048510	Biological Process	regulation of timing of transition from vegetative to reproductive phase
GO:0055046	Biological Process	microgametogenesis
GO:0016602	Cellular Component	CCAAT-binding factor complex
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 290 aa Download sequence Send to blast
MQPKSGRGNE AEVNDHHPAD QQQQPMMYPE PWWKNNAAFG VIPPPSSGLP SNSSSLDCPN 60 GSESNDLHSA SEDGAAGAND AAWKDSSQAV TSSPSGLVFF PLLGFITVDH HGMEGSDPTH 120 VAASMHNQQP VQPPELVGHY MACVPNPYQD PYYAGMMGAY GHQPLGFRPY LGMPRERTAL 180 PLDITQEPVY VNAKQYEGIL RRRKARAKAE LERKVINRKP YLHESRHKHA MRRARASGGR 240 FAKKTEAEAA EDAAAAAAGR EREKGSATNS SGSEPVETDS NETFNSSGAP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4awl_A	2e-15	185	241	1	58	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	225	234	RHKHAMRRAR

Functional Description ? help Back to Top
Source	Description
UniProt	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00016.1_g00003.1

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018444539.1	1e-175	PREDICTED: nuclear transcription factor Y subunit A-1-like isoform X2
Refseq	XP_018444576.1	1e-175	PREDICTED: nuclear transcription factor Y subunit A-1-like isoform X2
Swissprot	Q9LXV5	1e-149	NFYA1_ARATH; Nuclear transcription factor Y subunit A-1
TrEMBL	A0A3N6T280	1e-164	A0A3N6T280_BRACR; Uncharacterized protein
STRING	Bo9g169310.1	1e-159	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5946	26	46

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G12840.3	1e-115	nuclear factor Y, subunit A1

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Siriwardana CL, et al. NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T. PLoS Genet., 2016. 12(12): p. e1006496 [PMID:27977687] Zhao H, et al. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. Front Plant Sci, 2016. 7: p. 2045 [PMID:28119722]