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

    Gene ID: 54436, updated on 10-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (8182072..8241103)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (8160457..8219878)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (8183799..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 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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    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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    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_2024_08

    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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