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    TAF4B TATA-box binding protein associated factor 4b [ Homo sapiens (human) ]

    Gene ID: 6875, updated on 2-Nov-2024

    Summary

    Official Symbol
    TAF4Bprovided by HGNC
    Official Full Name
    TATA-box binding protein associated factor 4bprovided by HGNC
    Primary source
    HGNC:HGNC:11538
    See related
    Ensembl:ENSG00000141384 MIM:601689; AllianceGenome:HGNC:11538
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPGF13; TAF2C2; TAFII105
    Summary
    TATA binding protein (TBP) and TBP-associated factors (TAFs) participate in the formation of the TFIID protein complex, which is involved in initiation of transcription of genes by RNA polymerase II. This gene encodes a cell type-specific TAF that may be responsible for mediating transcription by a subset of activators in B cells. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
    Expression
    Broad expression in testis (RPKM 5.0), lymph node (RPKM 3.4) and 24 other tissues See more
    Orthologs
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    Genomic context

    See TAF4B in Genome Data Viewer
    Location:
    18q11.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26226445..26391685)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (26421246..26585805)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (23806409..23971649)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene proteasome 20S subunit alpha 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13180 Neighboring gene dihydrofolate reductase pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23787469-23787645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9371 Neighboring gene nucleophosmin 1 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23812073-23812268 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23824799-23825157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:23841243-23841743 Neighboring gene SINHCAF pseudogene 1 Neighboring gene MPRA-validated peak3086 silencer Neighboring gene uncharacterized LOC124904383 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23918413-23918607 Neighboring gene zinc finger protein 347 pseudogene Neighboring gene RNA, U6 small nuclear 1289, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23973056-23973249 Neighboring gene uncharacterized LOC107985142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13183 Neighboring gene long intergenic non-protein coding RNA 1543

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Spermatogenic failure 13
    MedGen: C4014449 OMIM: 615841 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Interaction of TFIID with the HIV-1 LTR, and therefore presumably HIV-1 Tat protein, is primarily dependent on the LTR TATA element and may also be stabilized or regulated by flanking E box motifs and basic helix-loop-helix proteins such as AP-4 and E47 PubMed
    tat TATA binding protein (TBP)-associated factors (TAFs) in the TFIID complex are required for activation by transcription factors, but are dispensable for HIV-1 Tat LTR transactivation function PubMed
    tat A novel function of LBP-1, restricting HIV-1 transcription at the level of elongation by preventing the binding of TFIID to the promoter, is suppressed by HIV-1 Tat, indicating Tat helps recruit TFIID to the HIV-1 LTR PubMed
    tat HIV-1 Tat stabilizes the interaction of TFIIA with TFIID, and TFIIA and TFIID are required to reconstitute Tat-specific and TAR-dependent activation of HIV transcription in vitro PubMed
    tat HIV-1 Tat binds, through amino acids 36-50, directly to the TBP subunit of the TFIID holoenzyme complex (which includes at least TFIID subunits p250, p125, p70, TBP, and p30), and increases the interaction of TFIID with the HIV-1 LTR promoter PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables NF-kappaB binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    contributes_to RNA polymerase II general transcription initiation factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II general transcription initiation factor activity IC
    Inferred by Curator
    more info
    PubMed 
    enables protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in RNA polymerase II preinitiation complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in oogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription initiation by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription initiation at RNA polymerase II promoter IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of transcription factor TFIID complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of transcription factor TFIID complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription factor TFIID complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    transcription initiation factor TFIID subunit 4B
    Names
    TAF(II)105
    TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa
    TATA box binding protein (TBP)-associated factor 4B
    TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD
    transcription initiation factor TFIID 105 kDa subunit

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_034162.1 RefSeqGene

      Range
      4563..169803
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001293725.2NP_001280654.1  transcription initiation factor TFIID subunit 4B isoform 1

      See identical proteins and their annotated locations for NP_001280654.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC016839, AC121320, AY888048, BC016360
      Consensus CDS
      CCDS77170.1
      UniProtKB/TrEMBL
      A4PBF7, J3KTH2
      Related
      ENSP00000462980.1, ENST00000578121.5
      Conserved Domains (2) summary
      pfam05236
      Location:621862
      TAF4; Transcription initiation factor TFIID component TAF4 family
      pfam07531
      Location:258346
      TAFH; NHR1 homology to TAF
    2. NM_005640.3NP_005631.1  transcription initiation factor TFIID subunit 4B isoform 2

      See identical proteins and their annotated locations for NP_005631.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC016839, AY888048, BC016360
      Consensus CDS
      CCDS42421.1
      UniProtKB/Swiss-Prot
      Q29YA4, Q29YA5, Q92750
      UniProtKB/TrEMBL
      A4PBF7
      Related
      ENSP00000269142.6, ENST00000269142.10
      Conserved Domains (2) summary
      pfam05236
      Location:616857
      TAF4; Transcription initiation factor TFIID component TAF4 family
      pfam07531
      Location:258346
      TAFH; NHR1 homology to TAF

    RNA

    1. NR_121653.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon and uses an alternate splice junction at the 5' end of an exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC016839, AC121320, AY888048, BC016360
      Related
      ENST00000418698.3

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      26226445..26391685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451239.2XP_024307007.1  transcription initiation factor TFIID subunit 4B isoform X1

      UniProtKB/TrEMBL
      A4PBF7
      Conserved Domains (3) summary
      pfam05236
      Location:616801
      TAF4; Transcription initiation factor TFIID component TAF4 family
      pfam07531
      Location:258346
      TAFH; NHR1 homology to TAF
      cl26464
      Location:14154
      Atrophin-1; Atrophin-1 family
    2. XM_011526153.3XP_011524455.1  transcription initiation factor TFIID subunit 4B isoform X4

      Conserved Domains (1) summary
      pfam07531
      Location:258346
      TAFH; NHR1 homology to TAF
    3. XM_017025932.2XP_016881421.1  transcription initiation factor TFIID subunit 4B isoform X3

    4. XM_005258339.4XP_005258396.1  transcription initiation factor TFIID subunit 4B isoform X2

      Conserved Domains (1) summary
      pfam07531
      Location:258346
      TAFH; NHR1 homology to TAF

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      26421246..26585805
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319037.1XP_054175012.1  transcription initiation factor TFIID subunit 4B isoform X1

    2. XM_054319041.1XP_054175016.1  transcription initiation factor TFIID subunit 4B isoform X5

      UniProtKB/TrEMBL
      B4DYT3
    3. XM_054319040.1XP_054175015.1  transcription initiation factor TFIID subunit 4B isoform X4

    4. XM_054319039.1XP_054175014.1  transcription initiation factor TFIID subunit 4B isoform X3

    5. XM_054319038.1XP_054175013.1  transcription initiation factor TFIID subunit 4B isoform X2