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Protein

RNA polymerase sigma factor sigC

Gene

SIGC

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

Functioni

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi531 – 55020H-T-H motifBy similarityAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • DNA-directed RNA polymerase activity Source: TAIR
  • plastid sigma factor activity Source: UniProtKB
  • sigma factor activity Source: TAIR
  • transcription factor activity, sequence-specific DNA binding Source: InterPro

GO - Biological processi

  • cellular response to light stimulus Source: UniProtKB
  • DNA-templated transcription, initiation Source: UniProtKB
  • regulation of RNA biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Sigma factor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor sigC
Short name:
Sigma factor C
Short name:
Sigma-C
Alternative name(s):
RNA polymerase sigma factor sig3
Short name:
Atsig3
Short name:
Sigma factor 3
Gene namesi
Name:SIGC
Synonyms:SIG3
Ordered Locus Names:At3g53920
ORF Names:F5K20.220
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G53920.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3232ChloroplastSequence analysisAdd
BLAST
Chaini33 – 571539RNA polymerase sigma factor sigCPRO_0000418095Add
BLAST

Proteomic databases

PaxDbiO24621.
PRIDEiO24621.

PTM databases

iPTMnetiO24621.

Expressioni

Tissue specificityi

Highly expressed in leaves, to a lower extent in cotyledons, and barely expressed in roots. Present in seeds, seedlings and etiolated plantlets.4 Publications

Inductioni

Slightly induced by blue light, especially after dark adaptation.5 Publications

Gene expression databases

GenevisibleiO24621. AT.

Interactioni

Protein-protein interaction databases

STRINGi3702.AT3G53920.1.

Structurei

3D structure databases

ProteinModelPortaliO24621.
SMRiO24621. Positions 298-566.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi360 – 37314Polymerase core bindingAdd
BLAST

Sequence similaritiesi

Belongs to the sigma-70 factor family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IGEE. Eukaryota.
COG0568. LUCA.
HOGENOMiHOG000005804.
InParanoidiO24621.
KOiK03093.
OMAiFRMQLRE.
PhylomeDBiO24621.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR014284. RNA_pol_sigma-70_dom.
IPR000943. RNA_pol_sigma70.
IPR007627. RNA_pol_sigma70_r2.
IPR007624. RNA_pol_sigma70_r3.
IPR007630. RNA_pol_sigma70_r4.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR016262. RNA_pol_sigma_SigB/C/D/F.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PIRSFiPIRSF000767. RNA_pol_sigma_SigB/C/D. 1 hit.
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 1 hit.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02937. sigma70-ECF. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O24621-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASFNSFPIP KQIVGSSSSS SSSTSRPRIL VRSSLTSSMT STNSMLVFVH
60 70 80 90 100
PHPLIKHWLS LLRSDQTSFP IFVRIPMTSV VATRWSFLSS VKEESRIYQN
110 120 130 140 150
DSLKACGCAS VSPYTAQNNV YVELKDPKEN IGVGSAERSY SSRSMLQYNL
160 170 180 190 200
LAKNLLALEE TFVALDSVRM ERDIMLQMGK LGAAELFKTC LSRYRGSSIT
210 220 230 240 250
SCLSDTTELV DTTPNQQVFV SSRRKVKKKA RRSSVTAENG DQSSLPIGLR
260 270 280 290 300
TTWNNIDVPR VRRPPKYRKK RERISRNETE MSTGVKIVAD MERIRTQLEE
310 320 330 340 350
ESGKVASLSC WAAAAGMNEK LLMRNLHYGW YCRDELVKST RSLVLFLARN
360 370 380 390 400
YRGLGIAHED LIQAGYVGVL QGAERFDHTR GYKFSTYVQY WIRKSMSTMV
410 420 430 440 450
SRHARGVHIP SSIIRTINHI QKARKTLKTS HGIKYAADEE IAKLTGHSVK
460 470 480 490 500
KIRAANQCLK VVGSIDKKVG DCFTTKFLEF TPDTTMESPE EAVMRQSARR
510 520 530 540 550
DIHDLLEGLE PREKQVMVLR YGLQDYRPKS LEEIGKLLKV SKEWIRKIER
560 570
RAMAKLRDQP NAEDLRYYLN Q
Length:571
Mass (Da):64,906
Last modified:January 1, 1998 - v1
Checksum:i7F1A1651D2B4D1DF
GO

Sequence cautioni

The sequence AAM91534.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti354 – 3541L → M in BAA22215 (PubMed:9405719).Curated
Sequence conflicti538 – 5381L → F in BAA22215 (PubMed:9405719).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D89994 mRNA. Translation: BAA22530.1.
AB019944 Genomic DNA. Translation: BAA82450.1.
AB004822 mRNA. Translation: BAA22215.1.
AF015544 mRNA. Translation: AAB69386.1.
AL132960 Genomic DNA. Translation: CAB88354.1.
CP002686 Genomic DNA. Translation: AEE79159.1.
BT030362 mRNA. Translation: ABO38775.1.
AY128331 mRNA. Translation: AAM91534.1. Different initiation.
PIRiT45932.
RefSeqiNP_190960.1. NM_115252.2.
UniGeneiAt.21270.

Genome annotation databases

EnsemblPlantsiAT3G53920.1; AT3G53920.1; AT3G53920.
GeneIDi824559.
GrameneiAT3G53920.1; AT3G53920.1; AT3G53920.
KEGGiath:AT3G53920.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D89994 mRNA. Translation: BAA22530.1.
AB019944 Genomic DNA. Translation: BAA82450.1.
AB004822 mRNA. Translation: BAA22215.1.
AF015544 mRNA. Translation: AAB69386.1.
AL132960 Genomic DNA. Translation: CAB88354.1.
CP002686 Genomic DNA. Translation: AEE79159.1.
BT030362 mRNA. Translation: ABO38775.1.
AY128331 mRNA. Translation: AAM91534.1. Different initiation.
PIRiT45932.
RefSeqiNP_190960.1. NM_115252.2.
UniGeneiAt.21270.

3D structure databases

ProteinModelPortaliO24621.
SMRiO24621. Positions 298-566.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT3G53920.1.

PTM databases

iPTMnetiO24621.

Proteomic databases

PaxDbiO24621.
PRIDEiO24621.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G53920.1; AT3G53920.1; AT3G53920.
GeneIDi824559.
GrameneiAT3G53920.1; AT3G53920.1; AT3G53920.
KEGGiath:AT3G53920.

Organism-specific databases

TAIRiAT3G53920.

Phylogenomic databases

eggNOGiENOG410IGEE. Eukaryota.
COG0568. LUCA.
HOGENOMiHOG000005804.
InParanoidiO24621.
KOiK03093.
OMAiFRMQLRE.
PhylomeDBiO24621.

Miscellaneous databases

PROiO24621.

Gene expression databases

GenevisibleiO24621. AT.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR014284. RNA_pol_sigma-70_dom.
IPR000943. RNA_pol_sigma70.
IPR007627. RNA_pol_sigma70_r2.
IPR007624. RNA_pol_sigma70_r3.
IPR007630. RNA_pol_sigma70_r4.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR016262. RNA_pol_sigma_SigB/C/D/F.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PIRSFiPIRSF000767. RNA_pol_sigma_SigB/C/D. 1 hit.
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 1 hit.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02937. sigma70-ECF. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of three cDNA species encoding plastid RNA polymerase sigma factors in Arabidopsis thaliana: evidence for the sigma factor heterogeneity in higher plant plastids."
    Tanaka K., Tozawa Y., Mochizuki N., Shinozaki K., Nagatani A., Wakasa K., Takahashi H.
    FEBS Lett. 413:309-313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], INDUCTION BY LIGHT, GENE FAMILY.
    Strain: cv. Columbia.
  2. "Leaf-specifically expressed genes for polypeptides destined for chloroplasts with domains of sigma70 factors of bacterial RNA polymerases in Arabidopsis thaliana."
    Isono K., Shimizu M., Yoshimoto K., Niwa Y., Satoh K., Yokota A., Kobayashi H.
    Proc. Natl. Acad. Sci. U.S.A. 94:14948-14953(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION BY LIGHT, GENE FAMILY.
    Strain: cv. Columbia.
    Tissue: Leaf.
  3. "The role of sigma factors in plastid transcription."
    Allison L.A.
    Biochimie 82:537-548(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, INDUCTION BY LIGHT, GENE FAMILY, NOMENCLATURE.
    Strain: cv. Columbia.
    Tissue: Seedling hypocotyl.
  4. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
    Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
    , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  5. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  6. "Arabidopsis ORF clones."
    Bautista V.R., Kim C.J., Chen H., Wu S.Y., De Los Reyes C., Ecker J.R.
    Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  7. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 224-571.
    Strain: cv. Columbia.
  8. Cited for: SUBCELLULAR LOCATION.
  9. "Evolutionary conservation of C-terminal domains of primary sigma(70)-type transcription factors between plants and bacteria."
    Hakimi M.-A., Privat I., Valay J.-G., Lerbs-Mache S.
    J. Biol. Chem. 275:9215-9221(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "Blue light specific and differential expression of a plastid sigma factor, Sig5 in Arabidopsis thaliana."
    Tsunoyama Y., Morikawa K., Shiina T., Toyoshima Y.
    FEBS Lett. 516:225-228(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY LIGHT.
    Strain: cv. Columbia.
  11. "Characterization of Arabidopsis plastid sigma-like transcription factors SIG1, SIG2 and SIG3."
    Privat I., Hakimi M.-A., Buhot L., Favory J.-J., Mache-Lerbs S.
    Plant Mol. Biol. 51:385-399(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    Strain: cv. Columbia.
  12. "A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons."
    Ishizaki Y., Tsunoyama Y., Hatano K., Ando K., Kato K., Shinmyo A., Kobori M., Takeba G., Nakahira Y., Shiina T.
    Plant J. 42:133-144(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  13. "Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters."
    Onda Y., Yagi Y., Saito Y., Takenaka N., Toyoshima Y.
    Plant J. 55:968-978(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY LIGHT.

Entry informationi

Entry nameiSIGC_ARATH
AccessioniPrimary (citable) accession number: O24621
Secondary accession number(s): O22058, Q8L7P7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2012
Last sequence update: January 1, 1998
Last modified: February 17, 2016
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.