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

AT1G03790.1

Common Name

AtTZF4, F11M21.28, SOM, TZF4

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 393aa MW: 43614.5 Da PI: 7.9029

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G03790.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	33.6	6.5e-11	125	148	3	26
S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHg 26 e C+ f+r+G C++Gd C FaHg AT1G03790.1 125 GEVCPEFRRGGDCSRGDDCEFAHG 148 689********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	13.535	122	150	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	3.79E-6	122	152	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	8.4E-6	122	149	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.9E-8	126	148	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	2.1E-6	126	150	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.5	158	181	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010187	Biological Process	negative regulation of seed germination
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046872	Molecular Function	metal ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009001	anatomy	fruit
PO:0009010	anatomy	seed
PO:0009030	anatomy	carpel
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 393 aa Download sequence Send to blast
MDVVCTEHQM RKPTVEIPPR KLLLSSKSFP SDSSSPRSPR KHNWNKSNKI TSEHEEDNED 60 NNRENKEYCY DSDSDDPYAS DHFRMFEFKI RRCTRSRSHD WTDCPFAHPG EKARRRDPRR 120 FQYSGEVCPE FRRGGDCSRG DDCEFAHGVF ECWLHPIRYR TEACKDGKHC KRKVCFFAHS 180 PRQLRVLPPE NVSGVSASPS PAAKNPCCLF CSSSPTSTLL GNLSHLSRSP SLSPPMSPAN 240 KAAAFSRLRN RAASAVSAAA AAGSMNYKDV LSELVNSLDS MSLAEALQAS SSSPVTTPVS 300 AAAAAFASSC GLSNQRLHLQ QQQPSSPLQF ALSPSTPSYL TNSPQANFFS DDFTPRRRQM 360 NDFTAMTAVR ENTNIEDGSC GDPDLGWVND LLT

Sequence ? help Back to Top

Protein Sequence Length: 393 aa Download sequence Send to blast

MDVVCTEHQM RKPTVEIPPR KLLLSSKSFP SDSSSPRSPR KHNWNKSNKI TSEHEEDNED  60
NNRENKEYCY DSDSDDPYAS DHFRMFEFKI RRCTRSRSHD WTDCPFAHPG EKARRRDPRR  120
FQYSGEVCPE FRRGGDCSRG DDCEFAHGVF ECWLHPIRYR TEACKDGKHC KRKVCFFAHS  180
PRQLRVLPPE NVSGVSASPS PAAKNPCCLF CSSSPTSTLL GNLSHLSRSP SLSPPMSPAN  240
KAAAFSRLRN RAASAVSAAA AAGSMNYKDV LSELVNSLDS MSLAEALQAS SSSPVTTPVS  300
AAAAAFASSC GLSNQRLHLQ QQQPSSPLQF ALSPSTPSYL TNSPQANFFS DDFTPRRRQM  360
NDFTAMTAVR ENTNIEDGSC GDPDLGWVND LLT

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.43010	0.0	seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	265084_at	0.0
Expression Atlas	AT1G03790	-
AtGenExpress	AT1G03790	-
ATTED-II	AT1G03790	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Specifically expressed in seeds. {ECO:0000269\|PubMed:18487351}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes SOMNUS (SOM), a nucleus-localized CCCH-type zinc finger protein. SOM negatively regulates light-dependent seed germination downstream of PIL5 (AT2G20180).
UniProt	Probable transcription repressor that functions as negative regulator of phytochrome-mediated promotion of seed germination. Inhibits seed germination by regulating the expression of gibberellic acid (GA) and abscisic acid (ABA) metabolic genes. Does not regulate the expression of the DELLA genes RGA and RGA1. Activated by PIL5, a phytochrome-interacting basic helix-loop-helix transcription factor. {ECO:0000269\|PubMed:18487351}.

Function -- GeneRIF ? help Back to Top
ABI3 and PIL5 collaboratively activate the expression of SOM mRNA by directly binding to and interacting with each other at the SOM promoter. [PMID: 21467583] AtTZF4, 5 and 6 affect seed germination by controlling genes critical for abscisic acid (ABA) and gibberellic acid (GA) response. [PMID: 23421766] ABI3, ABI5, and DELLAs mediate high-temperature signaling to activate the expression of SOM and other high-temperature-inducible genes, thereby inhibiting seed germination. [PMID: 24326588] SOM is reported to negatively regulate seeds germination by altering GA/ABA metabolism, here we found that AFP2 and ABI5 altered SOM transcription. Data demonstrate that AFP2 is a novel regulator to control high temperature-induced secondary seed dormancy through ABI5 and SOM. [PMID: 29723526]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G03790.1

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT2G20180 (A), AT3G24650 (A)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G03790

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC003027	0.0	AC003027.1 Arabidopsis thaliana chromosome I BAC F21M11 genomic sequence, complete sequence.
GenBank	CP002684	0.0	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_171875.1	0.0	Zinc finger C-x8-C-x5-C-x3-H type family protein
Swissprot	Q9ZWA1	0.0	C3H2_ARATH; Zinc finger CCCH domain-containing protein 2
TrEMBL	A0A178W4T9	0.0	A0A178W4T9_ARATH; TZF4
STRING	AT1G03790.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2987	27	66
Representative plant	OGRP1170	16	44

Link Out ? help Back to Top
Phytozome	AT1G03790.1
Entrez Gene	839408
iHOP	AT1G03790
wikigenes	AT1G03790

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Seki M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science, 2002. 296(5565): p. 141-5 [PMID:11910074] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Yazaki J, et al. Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol. Genomics, 2004. 17(2): p. 87-100 [PMID:14982972] Becerra C,Puigdomenech P,Vicient CM Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development. BMC Genomics, 2006. 7: p. 38 [PMID:16504176] Wang D, et al. Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics, 2008. 9: p. 44 [PMID:18221561] Kim DH, et al. SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5. Plant Cell, 2008. 20(5): p. 1260-77 [PMID:18487351] Pomeranz M,Lin PC,Finer J,Jang JC AtTZF gene family localizes to cytoplasmic foci. Plant Signal Behav, 2010. 5(2): p. 190-2 [PMID:20173417] Park J,Lee N,Kim W,Lim S,Choi G ABI3 and PIL5 collaboratively activate the expression of SOMNUS by directly binding to its promoter in imbibed Arabidopsis seeds. Plant Cell, 2011. 23(4): p. 1404-15 [PMID:21467583] Cho JN, et al. Control of seed germination by light-induced histone arginine demethylation activity. Dev. Cell, 2012. 22(4): p. 736-48 [PMID:22483719] Lee KP, et al. Spatially and genetically distinct control of seed germination by phytochromes A and B. Genes Dev., 2012. 26(17): p. 1984-96 [PMID:22948663] Renault H, et al. γ-Aminobutyric acid transaminase deficiency impairs central carbon metabolism and leads to cell wall defects during salt stress in Arabidopsis roots. Plant Cell Environ., 2013. 36(5): p. 1009-18 [PMID:23148892] Bogamuwa S,Jang JC The Arabidopsis tandem CCCH zinc finger proteins AtTZF4, 5 and 6 are involved in light-, abscisic acid- and gibberellic acid-mediated regulation of seed germination. Plant Cell Environ., 2013. 36(8): p. 1507-19 [PMID:23421766] Lim S, et al. ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis. Plant Cell, 2013. 25(12): p. 4863-78 [PMID:24326588] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Bogamuwa S,Jang JC Plant Tandem CCCH Zinc Finger Proteins Interact with ABA, Drought, and Stress Response Regulators in Processing-Bodies and Stress Granules. PLoS ONE, 2016. 11(3): p. e0151574 [PMID:26978070] Chang G, et al. AFP2 as the novel regulator breaks high-temperature-induced seeds secondary dormancy through ABI5 and SOM in Arabidopsis thaliana. Biochem. Biophys. Res. Commun., 2018. 501(1): p. 232-238 [PMID:29723526]