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Protein

TATA box-binding protein-associated factor RNA polymerase I subunit D

Gene

Taf1d

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation probably is primarily dependent on the rate of association of SL1/TIF-IB with the rDNA promoter. SL1/TIF-IB is involved in stabilization of nucleolar transcription factor 1/UBTF on rDNA. Formation of SL1/TIF-IB excludes the association of TBP with TFIID subunits (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-427359. SIRT1 negatively regulates rRNA Expression.
R-MMU-5250924. B-WICH complex positively regulates rRNA expression.
R-MMU-73762. RNA Polymerase I Transcription Initiation.
R-MMU-73772. RNA Polymerase I Promoter Escape.
R-MMU-73777. RNA Polymerase I Chain Elongation.
R-MMU-73863. RNA Polymerase I Transcription Termination.

Names & Taxonomyi

Protein namesi
Recommended name:
TATA box-binding protein-associated factor RNA polymerase I subunit D
Alternative name(s):
TATA box-binding protein-associated factor 1D
Short name:
TBP-associated factor 1D
Transcription initiation factor SL1/TIF-IB subunit D
Gene namesi
Name:Taf1d
Synonyms:Josd3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:1922566. Taf1d.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 322322TATA box-binding protein-associated factor RNA polymerase I subunit DPRO_0000250718Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei23 – 231PhosphoserineBy similarity
Modified residuei137 – 1371PhosphoserineBy similarity
Modified residuei232 – 2321PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9D4V4.
PeptideAtlasiQ9D4V4.
PRIDEiQ9D4V4.

PTM databases

iPTMnetiQ9D4V4.
PhosphoSiteiQ9D4V4.

Expressioni

Gene expression databases

BgeeiQ9D4V4.
GenevisibleiQ9D4V4. MM.

Interactioni

Subunit structurei

Component of the transcription factor SL1/TIF-IB complex, composed of TBP and at least TAF1A, TAF1B, TAF1C and TAF1D. Interacts with UBTF (By similarity).By similarity

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000034415.

Structurei

3D structure databases

ProteinModelPortaliQ9D4V4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Phylogenomic databases

eggNOGiENOG410IZI3. Eukaryota.
ENOG41124VA. LUCA.
GeneTreeiENSGT00390000009061.
HOGENOMiHOG000154498.
HOVERGENiHBG096071.
InParanoidiQ9D4V4.
KOiK15215.
OMAiSKIPECA.
OrthoDBiEOG7SV0WX.
PhylomeDBiQ9D4V4.
TreeFamiTF335756.

Family and domain databases

InterProiIPR027976. TAF1D.
[Graphical view]
PANTHERiPTHR14562. PTHR14562. 1 hit.
PfamiPF15333. TAF1D. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9D4V4-1) [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
MAQSEVNSVC VASDRAGDTG DQSDDSSDGS LFKTQCAPSP IQKQRHPTVK
60 70 80 90 100
RVTLPASVET DSSSDSSIEP RPLTLKAIFE RFKKKKRKKR KKRKYEPKLR
110 120 130 140 150
PRGRPRGKPS GTRITRRSQI DAKQIKDKGA VFPFLESESG RKPLPWKKIL
160 170 180 190 200
TYEQAVARGF FHHIEKLKYE HHLKECLKQM HAGEDLEKED LDSRRHKYMD
210 220 230 240 250
DDGSLSPIEE PLTEDEATNP QAECDIKLVE DSCFIISSEF SRKRNLEQEK
260 270 280 290 300
IKKESTFSKK AKDATHREKG HRRTLKGNEH VTIEEDSRPQ PRPFAHLQSK
310 320
VMKKGELEYL EVHHLCGLSQ PL
Length:322
Mass (Da):36,977
Last modified:October 3, 2006 - v2
Checksum:iBDA75165CEC29301
GO
Isoform 2 (identifier: Q9D4V4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     286-322: DSRPQPRPFAHLQSKVMKKGELEYLEVHHLCGLSQPL → GKEHR

Show »
Length:290
Mass (Da):33,333
Checksum:i6B62160C9644531A
GO
Isoform 3 (identifier: Q9D4V4-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     286-322: DSRPQPRPFAHLQSKVMKKGELEYLEVHHLCGLSQPL → GLS

Show »
Length:288
Mass (Da):32,982
Checksum:i98A88644531A1757
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti8 – 81S → F in BAB29621 (PubMed:16141072).Curated
Sequence conflicti148 – 1481K → R in BAB29621 (PubMed:16141072).Curated
Sequence conflicti173 – 1731L → P in BAB29621 (PubMed:16141072).Curated
Sequence conflicti276 – 2761K → E in BAB30118 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei286 – 32237DSRPQ…LSQPL → GKEHR in isoform 2. 1 PublicationVSP_020729Add
BLAST
Alternative sequencei286 – 32237DSRPQ…LSQPL → GLS in isoform 3. 2 PublicationsVSP_020730Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK050165 mRNA. Translation: BAC34104.1.
AK012662 mRNA. Translation: BAB28391.1.
AK014920 mRNA. Translation: BAB29621.1.
AK016109 mRNA. Translation: BAB30118.1.
AK166329 mRNA. Translation: BAE38709.1.
BC110660 mRNA. Translation: AAI10661.1.
BC117068 mRNA. Translation: AAI17069.1.
BC117070 mRNA. Translation: AAI17071.1.
CCDSiCCDS22836.1. [Q9D4V4-1]
CCDS52726.1. [Q9D4V4-2]
RefSeqiNP_081537.1. NM_027261.3. [Q9D4V4-2]
NP_083524.2. NM_029248.2. [Q9D4V4-1]
XP_006510726.1. XM_006510663.2. [Q9D4V4-1]
XP_011240922.1. XM_011242620.1. [Q9D4V4-1]
UniGeneiMm.354115.

Genome annotation databases

EnsembliENSMUST00000034415; ENSMUSP00000034415; ENSMUSG00000031939. [Q9D4V4-1]
ENSMUST00000164079; ENSMUSP00000129141; ENSMUSG00000031939. [Q9D4V4-2]
GeneIDi75316.
KEGGimmu:75316.
UCSCiuc009ofp.2. mouse. [Q9D4V4-1]
uc009ofq.2. mouse. [Q9D4V4-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK050165 mRNA. Translation: BAC34104.1.
AK012662 mRNA. Translation: BAB28391.1.
AK014920 mRNA. Translation: BAB29621.1.
AK016109 mRNA. Translation: BAB30118.1.
AK166329 mRNA. Translation: BAE38709.1.
BC110660 mRNA. Translation: AAI10661.1.
BC117068 mRNA. Translation: AAI17069.1.
BC117070 mRNA. Translation: AAI17071.1.
CCDSiCCDS22836.1. [Q9D4V4-1]
CCDS52726.1. [Q9D4V4-2]
RefSeqiNP_081537.1. NM_027261.3. [Q9D4V4-2]
NP_083524.2. NM_029248.2. [Q9D4V4-1]
XP_006510726.1. XM_006510663.2. [Q9D4V4-1]
XP_011240922.1. XM_011242620.1. [Q9D4V4-1]
UniGeneiMm.354115.

3D structure databases

ProteinModelPortaliQ9D4V4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000034415.

PTM databases

iPTMnetiQ9D4V4.
PhosphoSiteiQ9D4V4.

Proteomic databases

PaxDbiQ9D4V4.
PeptideAtlasiQ9D4V4.
PRIDEiQ9D4V4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000034415; ENSMUSP00000034415; ENSMUSG00000031939. [Q9D4V4-1]
ENSMUST00000164079; ENSMUSP00000129141; ENSMUSG00000031939. [Q9D4V4-2]
GeneIDi75316.
KEGGimmu:75316.
UCSCiuc009ofp.2. mouse. [Q9D4V4-1]
uc009ofq.2. mouse. [Q9D4V4-2]

Organism-specific databases

CTDi79101.
MGIiMGI:1922566. Taf1d.

Phylogenomic databases

eggNOGiENOG410IZI3. Eukaryota.
ENOG41124VA. LUCA.
GeneTreeiENSGT00390000009061.
HOGENOMiHOG000154498.
HOVERGENiHBG096071.
InParanoidiQ9D4V4.
KOiK15215.
OMAiSKIPECA.
OrthoDBiEOG7SV0WX.
PhylomeDBiQ9D4V4.
TreeFamiTF335756.

Enzyme and pathway databases

ReactomeiR-MMU-427359. SIRT1 negatively regulates rRNA Expression.
R-MMU-5250924. B-WICH complex positively regulates rRNA expression.
R-MMU-73762. RNA Polymerase I Transcription Initiation.
R-MMU-73772. RNA Polymerase I Promoter Escape.
R-MMU-73777. RNA Polymerase I Chain Elongation.
R-MMU-73863. RNA Polymerase I Transcription Termination.

Miscellaneous databases

ChiTaRSiTaf1d. mouse.
PROiQ9D4V4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9D4V4.
GenevisibleiQ9D4V4. MM.

Family and domain databases

InterProiIPR027976. TAF1D.
[Graphical view]
PANTHERiPTHR14562. PTHR14562. 1 hit.
PfamiPF15333. TAF1D. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
    Strain: C57BL/6J.
    Tissue: Liver, Mammary gland and Testis.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
    Strain: FVB/N.
    Tissue: Brain and Mammary tumor.
  3. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Spleen.

Entry informationi

Entry nameiTAF1D_MOUSE
AccessioniPrimary (citable) accession number: Q9D4V4
Secondary accession number(s): Q149X7
, Q8C7I5, Q9CZG0, Q9D5U6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 3, 2006
Last modified: July 6, 2016
This is version 97 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

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.