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Protein

Probable RNA polymerase II transcription factor B subunit 1-3

Gene

TFB1-3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Component of the general transcription and DNA repair factor IIH (TFIIH) core, which is essential for both basal and activated transcription, and is involved in nucleotide excision repair (NER) of damaged DNA.By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-5696395. Formation of Incision Complex in GG-NER.
R-ATH-5696400. Dual Incision in GG-NER.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-6781823. Formation of TC-NER Pre-Incision Complex.
R-ATH-6782135. Dual incision in TC-NER.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-ATH-72086. mRNA Capping.
R-ATH-73776. RNA Polymerase II Promoter Escape.
R-ATH-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-ATH-75953. RNA Polymerase II Transcription Initiation.
R-ATH-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-ATH-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable RNA polymerase II transcription factor B subunit 1-3
Alternative name(s):
General transcription and DNA repair factor IIH subunit TFB1-3
Short name:
AtTFB1-31 Publication
Short name:
TFIIH subunit TFB1-3
Gene namesi
Name:TFB1-3Curated
Synonyms:GTF2H1-2Curated
Ordered Locus Names:At3g61420
ORF Names:F2A19.20
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

TAIRiAT3G61420.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 579579Probable RNA polymerase II transcription factor B subunit 1-3PRO_0000406093Add
BLAST

Proteomic databases

PaxDbiQ9M322.
PRIDEiQ9M322.

Expressioni

Gene expression databases

GenevisibleiQ9M322. AT.

Interactioni

Subunit structurei

Component of the TFIIH core complex, which is composed of 7 subunits, XPD, XPB, TFB1/GTF2H1, GTF2H2/P44, TFB4/GTF2H3, TFB2/GTF2H4 and TFB5/GTF2H5.1 Publication

Protein-protein interaction databases

STRINGi3702.AT3G61420.1.

Structurei

3D structure databases

ProteinModelPortaliQ9M322.
SMRiQ9M322. Positions 4-102.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 16155BSD 1PROSITE-ProRule annotationAdd
BLAST
Domaini186 – 23853BSD 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 2 BSD domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2074. Eukaryota.
ENOG410XRI6. LUCA.
HOGENOMiHOG000006252.
InParanoidiQ9M322.
KOiK03141.
OMAiGRSHIFE.
PhylomeDBiQ9M322.

Family and domain databases

Gene3Di2.30.29.30. 1 hit.
InterProiIPR005607. BSD_dom.
IPR011993. PH_dom-like.
IPR027079. Tfb1/p62.
IPR013876. TFIIH_BTF_p62_N.
[Graphical view]
PANTHERiPTHR12856. PTHR12856. 1 hit.
PfamiPF03909. BSD. 1 hit.
PF08567. PH_TFIIH. 1 hit.
[Graphical view]
SMARTiSM00751. BSD. 2 hits.
[Graphical view]
SUPFAMiSSF50729. SSF50729. 1 hit.
PROSITEiPS50858. BSD. 2 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9M322-1) [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
MEKRVKYKSF VKDPGTLGSL ELSEVMLLFV PNDPKSDLKL KVQTHNIKSQ
60 70 80 90 100
KYTKEGSNKP PWLNLTSKQG RSHIFEFENY PDMHACRDFI TKALAKCEEE
110 120 130 140 150
PNKLVVLTPA EQLSMAEFEL RFKLLRENSE LQKLHKQFVE SKVLTEDEFW
160 170 180 190 200
STRKKLLGKD SIRKSKQQMG LKSMMVSGIK PSTDGRTNRV TFNLTSEIIF
210 220 230 240 250
QIFAEKPAVR QAFINYVPKK MTEKDFWTKY FRAEYLYSTK NTAVAAAEAA
260 270 280 290 300
EDEELAVFLK PDEILAQEAR QKMRRVDPTL DMDADEGDDY THLMDHGIQR
310 320 330 340 350
DGTNDIIEPQ NDQLKRSLLQ DLNRHAAVVL EGRCINVQSE DTRIVAEALT
360 370 380 390 400
RAKQVSKADG EITKDANQER LERMSRATEM EDLQAPQNFP LAPLSIKDPR
410 420 430 440 450
DYFESQQGNI LSEPRGAKAS KRNVHEAYGL LKESILVIRM TGLSDPLIKP
460 470 480 490 500
EVSFEVFSSL TRTISTAKNI LGKNPQESFL DRLPKSTKDE VIHHWTSIQE
510 520 530 540 550
LVRHFWSSYP ITTTYLSTKV GKLKDAMSNT YSLLDAMKQS VQSDLRHQVS
560 570
LLVRPMQQAL DAAFQHYESD LQRRTAKIT
Length:579
Mass (Da):66,386
Last modified:March 8, 2011 - v2
Checksum:iCF2071FDF0448608
GO
Isoform 2 (identifier: Q9M322-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     316-332: RSLLQDLNRHAAVVLEG → SIKNSHQMTSQQIVDEG
     333-579: Missing.

Show »
Length:332
Mass (Da):38,354
Checksum:iCB011A7D504385B9
GO
Isoform 3 (identifier: Q9M322-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-335: Missing.
     336-346: NVQSEDTRIVA → MYFGPLLLVLG

Show »
Length:244
Mass (Da):27,680
Checksum:i0E8DC2533E93A38D
GO

Sequence cautioni

The sequence CAB71072.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 335335Missing in isoform 3. 1 PublicationVSP_040742Add
BLAST
Alternative sequencei316 – 33217RSLLQ…VVLEG → SIKNSHQMTSQQIVDEG in isoform 2. 1 PublicationVSP_040743Add
BLAST
Alternative sequencei333 – 579247Missing in isoform 2. 1 PublicationVSP_040744Add
BLAST
Alternative sequencei336 – 34611NVQSEDTRIVA → MYFGPLLLVLG in isoform 3. 1 PublicationVSP_040745Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL132962 Genomic DNA. Translation: CAB71072.1. Sequence problems.
CP002686 Genomic DNA. Translation: AEE80200.1.
AK176589 mRNA. Translation: BAD44352.1.
BT021122 mRNA. Translation: AAX22257.1.
PIRiT47934.
RefSeqiNP_191701.4. NM_116007.4. [Q9M322-1]
UniGeneiAt.50300.

Genome annotation databases

EnsemblPlantsiAT3G61420.1; AT3G61420.1; AT3G61420. [Q9M322-1]
GeneIDi825315.
KEGGiath:AT3G61420.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL132962 Genomic DNA. Translation: CAB71072.1. Sequence problems.
CP002686 Genomic DNA. Translation: AEE80200.1.
AK176589 mRNA. Translation: BAD44352.1.
BT021122 mRNA. Translation: AAX22257.1.
PIRiT47934.
RefSeqiNP_191701.4. NM_116007.4. [Q9M322-1]
UniGeneiAt.50300.

3D structure databases

ProteinModelPortaliQ9M322.
SMRiQ9M322. Positions 4-102.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT3G61420.1.

Proteomic databases

PaxDbiQ9M322.
PRIDEiQ9M322.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT3G61420.1; AT3G61420.1; AT3G61420. [Q9M322-1]
GeneIDi825315.
KEGGiath:AT3G61420.

Organism-specific databases

TAIRiAT3G61420.

Phylogenomic databases

eggNOGiKOG2074. Eukaryota.
ENOG410XRI6. LUCA.
HOGENOMiHOG000006252.
InParanoidiQ9M322.
KOiK03141.
OMAiGRSHIFE.
PhylomeDBiQ9M322.

Enzyme and pathway databases

ReactomeiR-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-5696395. Formation of Incision Complex in GG-NER.
R-ATH-5696400. Dual Incision in GG-NER.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-6781823. Formation of TC-NER Pre-Incision Complex.
R-ATH-6782135. Dual incision in TC-NER.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-ATH-72086. mRNA Capping.
R-ATH-73776. RNA Polymerase II Promoter Escape.
R-ATH-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-ATH-75953. RNA Polymerase II Transcription Initiation.
R-ATH-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-ATH-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

PROiQ9M322.

Gene expression databases

GenevisibleiQ9M322. AT.

Family and domain databases

Gene3Di2.30.29.30. 1 hit.
InterProiIPR005607. BSD_dom.
IPR011993. PH_dom-like.
IPR027079. Tfb1/p62.
IPR013876. TFIIH_BTF_p62_N.
[Graphical view]
PANTHERiPTHR12856. PTHR12856. 1 hit.
PfamiPF03909. BSD. 1 hit.
PF08567. PH_TFIIH. 1 hit.
[Graphical view]
SMARTiSM00751. BSD. 2 hits.
[Graphical view]
SUPFAMiSSF50729. SSF50729. 1 hit.
PROSITEiPS50858. BSD. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (SEP-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
    Strain: cv. Columbia.
  4. "Arabidopsis ORF clones."
    Kim C.J., Chen H., Cheuk R.F., Shinn P., Ecker J.R.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
  5. "Components of nucleotide excision repair and DNA damage tolerance in Arabidopsis thaliana."
    Kunz B.A., Anderson H.J., Osmond M.J., Vonarx E.J.
    Environ. Mol. Mutagen. 45:115-127(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: COMPONENT OF TFIIH CORE COMPLEX, NOMENCLATURE.

Entry informationi

Entry nameiTFB1C_ARATH
AccessioniPrimary (citable) accession number: Q9M322
Secondary accession number(s): Q5BIV2, Q67Y79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 8, 2011
Last sequence update: March 8, 2011
Last modified: June 8, 2016
This is version 83 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

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.