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

Gene ID: 8464, updated on 31-Jan-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
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Genomic context

See SUPT3H in Genome Data Viewer
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)

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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
    UniProtKB/TrEMBL
    Q5U608
  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

    UniProtKB/TrEMBL
    Q5U608
  2. XM_054356578.1XP_054212553.1  transcription initiation protein SPT3 homolog isoform X3

    UniProtKB/Swiss-Prot
    A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
    UniProtKB/TrEMBL
    Q5U608
  3. XM_054356577.1XP_054212552.1  transcription initiation protein SPT3 homolog isoform X2

    UniProtKB/TrEMBL
    Q5U608
  4. XM_054356575.1XP_054212550.1  transcription initiation protein SPT3 homolog isoform X2

    UniProtKB/TrEMBL
    Q5U608
  5. XM_054356580.1XP_054212555.1  transcription initiation protein SPT3 homolog isoform X3

    UniProtKB/Swiss-Prot
    A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
    UniProtKB/TrEMBL
    Q5U608
  6. XM_054356579.1XP_054212554.1  transcription initiation protein SPT3 homolog isoform X3

    UniProtKB/Swiss-Prot
    A6NKG9, B2R9Q5, O75486, O76066, Q5TAV9, Q86VN7
    UniProtKB/TrEMBL
    Q5U608
  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

    UniProtKB/TrEMBL
    A0A1B0GVT7
  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