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    SUPT3H SPT3 homolog, SAGA and STAGA complex component [ Homo sapiens (human) ]

    Gene ID: 8464, updated on 2-May-2024

    Summary

    Official Symbol
    SUPT3Hprovided by HGNC
    Official Full Name
    SPT3 homolog, SAGA and STAGA complex componentprovided by HGNC
    Primary source
    HGNC:HGNC:11466
    See related
    Ensembl:ENSG00000196284 MIM:602947; AllianceGenome:HGNC:11466
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPT3; SPT3L
    Summary
    Enables transcription coactivator activity. Involved in histone H3 acetylation and histone deubiquitination. Located in nucleoplasm. Part of SAGA complex and transcription factor TFTC complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 1.4), ovary (RPKM 1.0) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    6p21.1
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (44809057..45377934, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (44643948..45212744, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (44776794..45345671, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375075 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:44588544-44589128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44592119-44592626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44592627-44593135 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44594661-44595168 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44595169-44595676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44597530-44598150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44598773-44599392 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:44610400-44611599 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:44619143-44619644 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:44619645-44620144 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44634844-44635352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44636371-44636878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24641 Neighboring gene uncharacterized LOC124901325 Neighboring gene uncharacterized LOC101929770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24643 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44727363-44727954 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:44739389-44740008 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44838634-44839257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44846566-44847066 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91988 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:44897835-44898036 Neighboring gene NUDT19 pseudogene 4 Neighboring gene MPRA-validated peak5818 silencer Neighboring gene MPRA-validated peak5819 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:45029844-45030504 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:45030505-45031165 Neighboring gene MPRA-validated peak5820 silencer Neighboring gene poly(rC) binding protein 2 pseudogene Neighboring gene RNA binding motif protein 22 pseudogene 4 Neighboring gene MPRA-validated peak5821 silencer Neighboring gene MPRA-validated peak5822 silencer Neighboring gene microRNA 586 Neighboring gene RUNX2 P1 promoter region Neighboring gene MPRA-validated peak5825 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17265 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:45345603-45346146 Neighboring gene uncharacterized LOC124901324 Neighboring gene runt related transcription factor 2 polyalanine expansion region Neighboring gene RUNX family transcription factor 2 Neighboring gene NANOG hESC enhancer GRCh37_chr6:45413685-45414186 Neighboring gene Sharpr-MPRA regulatory region 695 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:45487956-45488510 Neighboring gene Sharpr-MPRA regulatory region 12811 Neighboring gene RUNX2 antisense RNA 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies susceptibility loci for ossification of the posterior longitudinal ligament of the spine.
    EBI GWAS Catalog
    Common variants at 6p21.1 are associated with large artery atherosclerotic stroke.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Identification of 15 loci influencing height in a Korean population.
    EBI GWAS Catalog
    Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog
    Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ35021

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of SAGA complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of SAGA complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription factor TFTC complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription factor TFTC complex NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription initiation protein SPT3 homolog
    Names
    SPT3-like protein
    suppressor of Ty 3 homolog

    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.

    mRNA and Protein(s)

    1. NM_001261823.2NP_001248752.1  transcription initiation protein SPT3 homolog isoform 3

      See identical proteins and their annotated locations for NP_001248752.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) encodes isoform 3.
      Source sequence(s)
      AK303838, AL360272, DA012115
      UniProtKB/TrEMBL
      B4E1H0
      Conserved Domains (2) summary
      pfam14961
      Location:2280
      BROMI; Broad-minded protein
      cl02176
      Location:123141
      TAF11; TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex
    2. NM_001350324.2NP_001337253.1  transcription initiation protein SPT3 homolog isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) encodes isoform 4.
      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272
      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    3. NM_001350325.2NP_001337254.1  transcription initiation protein SPT3 homolog isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) encodes isoform 5.
      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272
      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24114
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    4. NM_001350326.2NP_001337255.1  transcription initiation protein SPT3 homolog isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) encodes isoform 6.
      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272, AL499610
      UniProtKB/TrEMBL
      A0A1B0GVT7
      Conserved Domains (1) summary
      cl02174
      Location:1495
      TAF13; The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex
    5. NM_001350327.2NP_001337256.1  transcription initiation protein SPT3 homolog isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) encodes isoform 7.
      Source sequence(s)
      AL096865, AL161905, AL360272
      UniProtKB/TrEMBL
      A0A1B0GVT7
      Conserved Domains (2) summary
      cl02174
      Location:130
      TAF13; The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex
      pfam14961
      Location:88146
      BROMI; Broad-minded protein
    6. NM_001350329.2NP_001337258.1  transcription initiation protein SPT3 homolog isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variant 1, encodes isoform 1.
      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272
      Consensus CDS
      CCDS34465.1
      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    7. NM_003599.4NP_003590.1  transcription initiation protein SPT3 homolog isoform 1

      See identical proteins and their annotated locations for NP_003590.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1), as well as variant 8, encodes isoform 1.
      Source sequence(s)
      AF073930, AL360272, DA012115
      Consensus CDS
      CCDS34465.1
      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
      UniProtKB/TrEMBL
      Q5U608
      Related
      ENSP00000360514.1, ENST00000371459.6
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    8. NM_181356.3NP_852001.1  transcription initiation protein SPT3 homolog isoform 2

      See identical proteins and their annotated locations for NP_852001.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AL360272, BC050384, DA012115
      Consensus CDS
      CCDS34466.1
      Related
      ENSP00000360515.1, ENST00000371460.5
      Conserved Domains (3) summary
      pfam02269
      Location:46127
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
      pfam14961
      Location:185243
      BROMI; Broad-minded protein
      cl02176
      Location:286304
      TAF11; TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex

    RNA

    1. NR_146632.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272
    2. NR_146633.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272
    3. NR_146634.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272
    4. NR_146635.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL096865, AL138880, AL161905, AL360272

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      44809057..45377934 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514953.4XP_011513255.1  transcription initiation protein SPT3 homolog isoform X2

      See identical proteins and their annotated locations for XP_011513255.1

      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    2. XM_024446572.2XP_024302340.1  transcription initiation protein SPT3 homolog isoform X3

      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    3. XM_011514954.4XP_011513256.1  transcription initiation protein SPT3 homolog isoform X2

      See identical proteins and their annotated locations for XP_011513256.1

      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    4. XM_011514952.3XP_011513254.1  transcription initiation protein SPT3 homolog isoform X2

      See identical proteins and their annotated locations for XP_011513254.1

      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    5. XM_017011371.2XP_016866860.1  transcription initiation protein SPT3 homolog isoform X3

      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
      UniProtKB/TrEMBL
      Q5U608
      Conserved Domains (1) summary
      pfam02269
      Location:24116
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
    6. XM_047419416.1XP_047275372.1  transcription initiation protein SPT3 homolog isoform X3

      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
    7. XM_011514949.4XP_011513251.1  transcription initiation protein SPT3 homolog isoform X1

      Conserved Domains (3) summary
      pfam02269
      Location:46127
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
      pfam14961
      Location:185243
      BROMI; Broad-minded protein
      cl02176
      Location:286304
      TAF11; TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex
    8. XM_017011370.2XP_016866859.1  transcription initiation protein SPT3 homolog isoform X1

      Conserved Domains (3) summary
      pfam02269
      Location:46127
      TFIID-18kDa; Transcription initiation factor IID, 18kD subunit
      pfam14961
      Location:185243
      BROMI; Broad-minded protein
      cl02176
      Location:286304
      TAF11; TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex
    9. XM_017011374.3XP_016866863.1  transcription initiation protein SPT3 homolog isoform X5

      UniProtKB/TrEMBL
      A0A1B0GVT7
      Related
      ENSP00000490652.2, ENST00000637763.2
    10. XM_047419417.1XP_047275373.1  transcription initiation protein SPT3 homolog isoform X4

    RNA

    1. XR_007059345.1 RNA Sequence

    2. XR_926319.4 RNA Sequence

    3. XR_001743692.2 RNA Sequence

    4. XR_007059346.1 RNA Sequence

    5. XR_007059347.1 RNA Sequence

    6. XR_926321.1 RNA Sequence

    7. XR_926320.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      44643948..45212744 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356576.1XP_054212551.1  transcription initiation protein SPT3 homolog isoform X2

    2. XM_054356578.1XP_054212553.1  transcription initiation protein SPT3 homolog isoform X3

      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
    3. XM_054356577.1XP_054212552.1  transcription initiation protein SPT3 homolog isoform X2

    4. XM_054356575.1XP_054212550.1  transcription initiation protein SPT3 homolog isoform X2

    5. XM_054356580.1XP_054212555.1  transcription initiation protein SPT3 homolog isoform X3

      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
    6. XM_054356579.1XP_054212554.1  transcription initiation protein SPT3 homolog isoform X3

      UniProtKB/Swiss-Prot
      A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
    7. XM_054356573.1XP_054212548.1  transcription initiation protein SPT3 homolog isoform X1

    8. XM_054356574.1XP_054212549.1  transcription initiation protein SPT3 homolog isoform X1

    9. XM_054356582.1XP_054212557.1  transcription initiation protein SPT3 homolog isoform X5

    10. XM_054356572.1XP_054212547.1  transcription initiation protein SPT3 homolog isoform X1

    11. XM_054356581.1XP_054212556.1  transcription initiation protein SPT3 homolog isoform X4

    RNA

    1. XR_008487449.1 RNA Sequence

    2. XR_008487447.1 RNA Sequence

    3. XR_008487452.1 RNA Sequence

    4. XR_008487451.1 RNA Sequence

    5. XR_008487453.1 RNA Sequence

    6. XR_008487450.1 RNA Sequence

    7. XR_008487448.1 RNA Sequence