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SH3TC1 SH3 domain and tetratricopeptide repeats 1 [ Homo sapiens (human) ]

Gene ID: 54436, updated on 3-Apr-2024

Summary

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Official Symbol
SH3TC1provided by HGNC
Official Full Name
SH3 domain and tetratricopeptide repeats 1provided by HGNC
Primary source
HGNC:HGNC:26009
See related
Ensembl:ENSG00000125089 AllianceGenome:HGNC:26009
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
Expression
Broad expression in spleen (RPKM 7.5), kidney (RPKM 5.6) and 25 other tissues See more
Orthologs
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Genomic context

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See SH3TC1 in Genome Data Viewer
Location:
4p16.1
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (8182072..8241103)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (8160457..8219878)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (8201017..8242830)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene actin binding LIM protein family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8007792-8008380 Neighboring gene Sharpr-MPRA regulatory region 2931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8026198-8026721 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:8026730-8027230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8039172-8039672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8041509-8042464 Neighboring gene microRNA 95 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:8050961-8051572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8062037-8062764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8072999-8073862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8080453-8080952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:8086980-8087888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:8098780-8099499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8105045-8105756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8105757-8106466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8106467-8107176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8107177-8107886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:8110453-8111188 Neighboring gene Sharpr-MPRA regulatory region 605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8127946-8128570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8151878-8152752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8175771-8176270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8177753-8178598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8189546-8190072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8191649-8192174 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:8193227-8193751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21288 Neighboring gene guanine monophosphate synthase pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8207619-8208120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8208121-8208620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8210744-8211508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8217127-8217691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8217692-8218255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8228681-8229350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8230692-8231362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8239598-8240458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8240459-8241317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8243787-8244348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8246371-8246872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8253953-8254459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8254460-8254965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8261245-8261746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15262 Neighboring gene uncharacterized LOC105374373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8293385-8293884 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:8296956-8297199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8297405-8297904 Neighboring gene HtrA serine peptidase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8316207-8317036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:8317037-8317864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:8325636-8326136 Neighboring gene long intergenic non-protein coding RNA 2517

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. ZNF70, a novel ILDR2-interacting protein, contributes to the regulation of HES1 gene expression. Watanabe K, et al. Biochem Biophys Res Commun, 2016 Sep 2. PMID 27353377
  2. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Trynka G, et al. Gut, 2009 Aug. PMID 19240061
  3. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. Li X, et al. Mol Syst Biol, 2015 Jan 21. PMID 25609649, Free PMC Article
  4. High-throughput analyses of hnRNP H1 dissects its multi-functional aspect. Uren PJ, et al. RNA Biol, 2016. PMID 26760575, Free PMC Article
  5. Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. Kim JJ, et al. Genes Dev, 2019 Dec 1. PMID 31753913, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20356, FLJ32999, FLJ36243, FLJ46394

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  

General protein information

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Preferred Names
SH3 domain and tetratricopeptide repeat-containing protein 1
Names
SH3 domain and tetratricopeptide repeats-containing protein 1

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_001318480.2 → NP_001305409.2  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in its 5' UTR compared to variant 1. This variant represents translation initiation at a downstream start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream start codon to encode an isoform (2) that has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC104650, KF459594
    Consensus CDS
    CCDS93476.1
    UniProtKB/TrEMBL
    B3KWX8, H0YA34
    Conserved Domains (3) summary
    cd11885
    Location:233 → 287
    SH3_SH3TC; Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains
    sd00006
    Location:1077 → 1104
    TPR; TPR repeat [structural motif]
    pfam13424
    Location:1080 → 1148
    TPR_12; Tetratricopeptide repeat

  2. NM_001410712.1 → NP_001397641.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC104650, KF459594
    Consensus CDS
    CCDS93475.1
    UniProtKB/TrEMBL
    A0A804HI81

  3. NM_018986.5 → NP_061859.4  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC104650, KF459594
    Consensus CDS
    CCDS3399.1
    UniProtKB/Swiss-Prot
    Q4W5G5, Q8TE82
    UniProtKB/TrEMBL
    B3KWX8
    Related
    ENSP00000245105.3, ENST00000245105.8
    Conserved Domains (3) summary
    cd11885
    Location:309 → 363
    SH3_SH3TC; Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains
    sd00006
    Location:1153 → 1180
    TPR; TPR repeat [structural motif]
    pfam13424
    Location:1156 → 1224
    TPR_12; Tetratricopeptide repeat

RNA

  1. NR_134639.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate internal exons, 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)
    AC104650, KF459594
    Related
    ENST00000502669.5

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    8182072..8241103
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513488.1 → XP_011511790.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X3

    See identical proteins and their annotated locations for XP_011511790.1

    UniProtKB/Swiss-Prot
    Q4W5G5, Q8TE82
    UniProtKB/TrEMBL
    B3KWX8
    Conserved Domains (3) summary
    cd11885
    Location:309 → 363
    SH3_SH3TC; Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains
    sd00006
    Location:1153 → 1180
    TPR; TPR repeat [structural motif]
    pfam13424
    Location:1156 → 1224
    TPR_12; Tetratricopeptide repeat

  2. XM_047415792.1 → XP_047271748.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X4

    UniProtKB/TrEMBL
    A0A804HI81
    Related
    ENSP00000506945.1, ENST00000684698.1

  3. XM_047415790.1 → XP_047271746.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    H0YA34
    Related
    ENSP00000426035.2, ENST00000508641.2

  4. XM_024454094.2 → XP_024309862.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    B3KWX8
    Conserved Domains (3) summary
    sd00006
    Location:1050 → 1077
    TPR; TPR repeat [structural motif]
    pfam13424
    Location:1053 → 1121
    TPR_12; Tetratricopeptide repeat
    cl17036
    Location:233 → 269
    SH3; Src Homology 3 domain superfamily

  5. XM_047415794.1 → XP_047271750.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X5

    Related
    ENSP00000507811.1, ENST00000682056.1

  6. XM_047415791.1 → XP_047271747.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X3

    UniProtKB/Swiss-Prot
    Q4W5G5, Q8TE82

  7. XM_017008300.3 → XP_016863789.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X3

    UniProtKB/Swiss-Prot
    Q4W5G5, Q8TE82
    UniProtKB/TrEMBL
    B3KWX8
    Conserved Domains (3) summary
    cd11885
    Location:309 → 363
    SH3_SH3TC; Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains
    sd00006
    Location:1153 → 1180
    TPR; TPR repeat [structural motif]
    pfam13424
    Location:1156 → 1224
    TPR_12; Tetratricopeptide repeat

  8. XM_006713889.3 → XP_006713952.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    Q53GR6
    Conserved Domains (3) summary
    cd11885
    Location:138 → 192
    SH3_SH3TC; Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains
    sd00006
    Location:982 → 1009
    TPR; TPR repeat [structural motif]
    pfam13424
    Location:981 → 1051
    TPR_12; Tetratricopeptide repeat

  9. XM_047415795.1 → XP_047271751.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X7

  10. XM_006713891.4 → XP_006713954.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X7

    See identical proteins and their annotated locations for XP_006713954.1

    UniProtKB/TrEMBL
    Q53GR6
    Conserved Domains (3) summary
    cd11885
    Location:16 → 70
    SH3_SH3TC; Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains
    sd00006
    Location:860 → 887
    TPR; TPR repeat [structural motif]
    pfam13424
    Location:859 → 931
    TPR_12; Tetratricopeptide repeat

RNA

  1. XR_007057930.1 RNA Sequence

  2. XR_007057931.1 RNA Sequence

  3. XR_007057932.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    8160457..8219878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350203.1 → XP_054206178.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X3

  2. XM_054350204.1 → XP_054206179.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X4

  3. XM_054350199.1 → XP_054206174.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X1

  4. XM_054350200.1 → XP_054206175.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X2

  5. XM_054350205.1 → XP_054206180.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X5

  6. XM_054350206.1 → XP_054206181.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X8

  7. XM_054350207.1 → XP_054206182.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X9

  8. XM_054350209.1 → XP_054206184.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X10

  9. XM_054350202.1 → XP_054206177.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X3

  10. XM_054350201.1 → XP_054206176.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X3

  11. XM_054350208.1 → XP_054206183.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X6

  12. XM_054350210.1 → XP_054206185.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X7

  13. XM_054350211.1 → XP_054206186.1  SH3 domain and tetratricopeptide repeat-containing protein 1 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TE82.3 GenPept UniProtKB/Swiss-Prot:Q8TE82

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