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Protein

Auxin response factor 1

Gene

ARF1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Auxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Seems to act as transcriptional repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Acts as repressor of IAA2, IAA3 and IAA7.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi124 – 226103TF-B3PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: TAIR
  2. sequence-specific DNA binding transcription factor activity Source: TAIR

GO - Biological processi

  1. auxin-activated signaling pathway Source: UniProtKB-KW
  2. leaf senescence Source: TAIR
  3. negative regulation of transcription, DNA-templated Source: TAIR
  4. response to auxin Source: TAIR
  5. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Auxin signaling pathway, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Auxin response factor 1
Gene namesi
Name:ARF1
Ordered Locus Names:At1g59750
ORF Names:F23H11.7
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G59750.

Subcellular locationi

GO - Cellular componenti

  1. nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 665665Auxin response factor 1PRO_0000111505Add
BLAST

Proteomic databases

PRIDEiQ8L7G0.

Expressioni

Tissue specificityi

Expressed in the whole plant.1 Publication

Developmental stagei

Expressed in the sepals and carpels of young flower buds. At stage 10 of flower development, expression in the carpels becomes restricted to the style. Also expressed in anthers and filaments. At stage 13, expressed in the region at the top of the pedicel, including the abscission zone.1 Publication

Gene expression databases

ExpressionAtlasiQ8L7G0. baseline and differential.
GenevestigatoriQ8L7G0.

Interactioni

Subunit structurei

Homodimers and heterodimers. Interacts with the auxin-responsive proteins IAA12, IAA13, IAA17 and with ARF2.

Binary interactionsi

WithEntry#Exp.IntActNotes
F3A4.140Q9SN122EBI-2324259,EBI-2324225

Protein-protein interaction databases

BioGridi27493. 10 interactions.
IntActiQ8L7G0. 16 interactions.
MINTiMINT-7712748.
STRINGi3702.AT1G59750.1-P.

Structurei

Secondary structure

1
665
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi17 – 2812Combined sources
Beta strandi40 – 434Combined sources
Helixi45 – 528Combined sources
Beta strandi54 – 563Combined sources
Beta strandi71 – 8414Combined sources
Beta strandi86 – 883Combined sources
Beta strandi91 – 999Combined sources
Beta strandi121 – 1277Combined sources
Helixi130 – 1334Combined sources
Beta strandi134 – 1374Combined sources
Beta strandi139 – 1413Combined sources
Helixi143 – 1497Combined sources
Beta strandi157 – 1593Combined sources
Beta strandi161 – 1677Combined sources
Beta strandi173 – 1819Combined sources
Turni182 – 1854Combined sources
Beta strandi186 – 1894Combined sources
Helixi193 – 1997Combined sources
Beta strandi207 – 2137Combined sources
Beta strandi218 – 2214Combined sources
Helixi239 – 25618Combined sources
Beta strandi260 – 2645Combined sources
Turni266 – 2683Combined sources
Beta strandi274 – 2763Combined sources
Helixi277 – 2859Combined sources
Beta strandi293 – 2975Combined sources
Beta strandi301 – 3044Combined sources
Beta strandi307 – 31610Combined sources
Beta strandi321 – 3233Combined sources
Beta strandi331 – 3377Combined sources
Beta strandi345 – 3473Combined sources
Helixi349 – 3513Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4LDVX-ray1.45A1-355[»]
4LDWX-ray2.67A/B1-355[»]
4LDXX-ray2.90A/B1-355[»]
4LDYX-ray2.30A/B1-355[»]
ProteinModelPortaliQ8L7G0.
SMRiQ8L7G0. Positions 15-355, 542-631.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini542 – 63594PB1PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi344 – 41269Pro-richAdd
BLAST

Domaini

Interactions between auxin response factors (ARFs) and Aux/IAA proteins occur through their C-terminal dimerization domains III and IV.

Sequence similaritiesi

Belongs to the ARF family.Curated
Contains 1 PB1 domain.PROSITE-ProRule annotation
Contains 1 TF-B3 DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG257828.
HOGENOMiHOG000241141.
InParanoidiQ8L7G0.
KOiK14486.
OMAiKVHWDEP.
PhylomeDBiQ8L7G0.

Family and domain databases

Gene3Di2.40.330.10. 1 hit.
InterProiIPR003311. AUX_IAA.
IPR011525. AuxIAA_ARF_dimer.
IPR010525. Auxin_resp.
IPR003340. B3_DNA-bd.
IPR015300. DNA-bd_pseudobarrel.
[Graphical view]
PfamiPF02309. AUX_IAA. 1 hit.
PF06507. Auxin_resp. 1 hit.
PF02362. B3. 1 hit.
[Graphical view]
SMARTiSM01019. B3. 1 hit.
[Graphical view]
SUPFAMiSSF101936. SSF101936. 1 hit.
PROSITEiPS50863. B3. 1 hit.
PS51745. PB1. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8L7G0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAASNHSSGK PGGVLSDALC RELWHACAGP LVTLPREGER VYYFPEGHME
60 70 80 90 100
QLEASMHQGL EQQMPSFNLP SKILCKVINI QRRAEPETDE VYAQITLLPE
110 120 130 140 150
LDQSEPTSPD APVQEPEKCT VHSFCKTLTA SDTSTHGGFS VLRRHADDCL
160 170 180 190 200
PPLDMSQQPP WQELVATDLH NSEWHFRHIF RGQPRRHLLT TGWSVFVSSK
210 220 230 240 250
KLVAGDAFIF LRGENEELRV GVRRHMRQQT NIPSSVISSH SMHIGVLATA
260 270 280 290 300
AHAITTGTIF SVFYKPRTSR SEFIVSVNRY LEAKTQKLSV GMRFKMRFEG
310 320 330 340 350
EEAPEKRFSG TIVGVQENKS SVWHDSEWRS LKVQWDEPSS VFRPERVSPW
360 370 380 390 400
ELEPLVANST PSSQPQPPQR NKRPRPPGLP SPATGPSGPV TPDGVWKSPA
410 420 430 440 450
DTPSSVPLFS PPAKAATFGH GGNKSFGVSI GSAFWPTNAD SAAESFASAF
460 470 480 490 500
NNESTEKKQT NGNVCRLFGF ELVENVNVDE CFSAASVSGA VAVDQPVPSN
510 520 530 540 550
EFDSGQQSEP LNINQSDIPS GSGDPEKSSL RSPQESQSRQ IRSCTKVHMQ
560 570 580 590 600
GSAVGRAIDL TRSECYEDLF KKLEEMFDIK GELLESTKKW QVVYTDDEDD
610 620 630 640 650
MMMVGDDPWN EFCGMVRKIF IYTPEEVKKL SPKNKLAVNA RMQLKADAEE
660
NGNTEGRSSS MAGSR
Length:665
Mass (Da):73,668
Last modified:April 13, 2004 - v2
Checksum:i79DD3180C2091401
GO
Isoform 2 (identifier: Q8L7G0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     390-392: Missing.

Note: May be due to a competing acceptor splice site. No experimental confirmation available.

Show »
Length:662
Mass (Da):73,370
Checksum:i598A0403F161FA54
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti136 – 1361H → Q in AAM91657 (PubMed:14593172).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei390 – 3923Missing in isoform 2. 1 PublicationVSP_010077

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U83245 mRNA. Translation: AAC49751.1.
AC007258 Genomic DNA. Translation: AAD39318.1.
CP002684 Genomic DNA. Translation: AEE33612.1.
CP002684 Genomic DNA. Translation: AEE33613.1.
CP002684 Genomic DNA. Translation: AEE33614.1.
AY133723 mRNA. Translation: AAM91657.1.
BT002748 mRNA. Translation: AAO22577.1.
PIRiD96621.
RefSeqiNP_001031208.1. NM_001036131.2. [Q8L7G0-1]
NP_176184.1. NM_104668.3. [Q8L7G0-1]
NP_849830.1. NM_179499.2. [Q8L7G0-2]
UniGeneiAt.74832.

Genome annotation databases

EnsemblPlantsiAT1G59750.1; AT1G59750.1; AT1G59750. [Q8L7G0-1]
AT1G59750.3; AT1G59750.3; AT1G59750. [Q8L7G0-1]
GeneIDi842268.
KEGGiath:AT1G59750.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U83245 mRNA. Translation: AAC49751.1.
AC007258 Genomic DNA. Translation: AAD39318.1.
CP002684 Genomic DNA. Translation: AEE33612.1.
CP002684 Genomic DNA. Translation: AEE33613.1.
CP002684 Genomic DNA. Translation: AEE33614.1.
AY133723 mRNA. Translation: AAM91657.1.
BT002748 mRNA. Translation: AAO22577.1.
PIRiD96621.
RefSeqiNP_001031208.1. NM_001036131.2. [Q8L7G0-1]
NP_176184.1. NM_104668.3. [Q8L7G0-1]
NP_849830.1. NM_179499.2. [Q8L7G0-2]
UniGeneiAt.74832.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4LDVX-ray1.45A1-355[»]
4LDWX-ray2.67A/B1-355[»]
4LDXX-ray2.90A/B1-355[»]
4LDYX-ray2.30A/B1-355[»]
ProteinModelPortaliQ8L7G0.
SMRiQ8L7G0. Positions 15-355, 542-631.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi27493. 10 interactions.
IntActiQ8L7G0. 16 interactions.
MINTiMINT-7712748.
STRINGi3702.AT1G59750.1-P.

Proteomic databases

PRIDEiQ8L7G0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G59750.1; AT1G59750.1; AT1G59750. [Q8L7G0-1]
AT1G59750.3; AT1G59750.3; AT1G59750. [Q8L7G0-1]
GeneIDi842268.
KEGGiath:AT1G59750.

Organism-specific databases

GeneFarmi3363. 345.
TAIRiAT1G59750.

Phylogenomic databases

eggNOGiNOG257828.
HOGENOMiHOG000241141.
InParanoidiQ8L7G0.
KOiK14486.
OMAiKVHWDEP.
PhylomeDBiQ8L7G0.

Gene expression databases

ExpressionAtlasiQ8L7G0. baseline and differential.
GenevestigatoriQ8L7G0.

Family and domain databases

Gene3Di2.40.330.10. 1 hit.
InterProiIPR003311. AUX_IAA.
IPR011525. AuxIAA_ARF_dimer.
IPR010525. Auxin_resp.
IPR003340. B3_DNA-bd.
IPR015300. DNA-bd_pseudobarrel.
[Graphical view]
PfamiPF02309. AUX_IAA. 1 hit.
PF06507. Auxin_resp. 1 hit.
PF02362. B3. 1 hit.
[Graphical view]
SMARTiSM01019. B3. 1 hit.
[Graphical view]
SUPFAMiSSF101936. SSF101936. 1 hit.
PROSITEiPS50863. B3. 1 hit.
PS51745. PB1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "ARF1, a transcription factor that binds to auxin response elements."
    Ulmasov T., Hagen G., Guilfoyle T.J.
    Science 276:1865-1868(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Strain: cv. Columbia.
  5. "Dimerization and DNA binding of auxin response factors."
    Ulmasov T., Hagen G., Guilfoyle T.J.
    Plant J. 19:309-319(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: DIMERIZATION, TISSUE SPECIFICITY.
  6. "Activation and repression of transcription by auxin-response factors."
    Ulmasov T., Hagen G., Guilfoyle T.J.
    Proc. Natl. Acad. Sci. U.S.A. 96:5844-5849(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: TRANSCRIPTIONAL REPRESSOR.
  7. "Auxin-responsive gene expression: genes, promoters and regulatory factors."
    Hagen G., Guilfoyle T.J.
    Plant Mol. Biol. 49:373-385(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE, FUNCTION.
  8. "AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana."
    Ellis C.M., Nagpal P., Young J.C., Hagen G., Guilfoyle T.J., Reed J.W.
    Development 132:4563-4574(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DEVELOPMENTAL STAGE.
  9. Cited for: GENE FAMILY.

Entry informationi

Entry nameiARFA_ARATH
AccessioniPrimary (citable) accession number: Q8L7G0
Secondary accession number(s): O23664
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2004
Last sequence update: April 13, 2004
Last modified: April 1, 2015
This is version 104 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.