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    TSSC4 tumor suppressing subtransferable candidate 4 [ Homo sapiens (human) ]

    Gene ID: 10078, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TSSC4provided by HGNC
    Official Full Name
    tumor suppressing subtransferable candidate 4provided by HGNC
    Primary source
    HGNC:HGNC:12386
    See related
    Ensembl:ENSG00000184281 MIM:603852; AllianceGenome:HGNC:12386
    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
    Summary
    This gene is one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. This gene is located among several imprinted genes; however, this gene, as well as the pan-hematopoietic expression gene (PHEMX), escapes imprinting. This gene may play a role in malignancies and disease that involve this region. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
    Expression
    Ubiquitous expression in testis (RPKM 10.6), bone marrow (RPKM 6.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TSSC4 in Genome Data Viewer
    Location:
    11p15.5
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (2400750..2403876)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (2490101..2493227)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (2421980..2425106)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene CD81 antisense RNA 1 Neighboring gene uncharacterized LOC105376520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2396527-2397285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2400391-2401372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2401373-2402355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4297 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4298 Neighboring gene nonconserved acetylation island sequence 93 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4301 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2421638-2422140 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2422141-2422641 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2435338-2435838 Neighboring gene Sharpr-MPRA regulatory region 9407 Neighboring gene CD81 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3070 Neighboring gene transient receptor potential cation channel subfamily M member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2482166-2482666 Neighboring gene Sharpr-MPRA regulatory region 11059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4304 Neighboring gene potassium voltage-gated channel subfamily Q member 1 Neighboring gene uncharacterized LOC124902613

    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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    Related articles in PubMed

    1. The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling. Bergfort A, et al. Nucleic Acids Res, 2022 Mar 21. PMID 35188580, Free PMC Article
    2. Two novel genes in the center of the 11p15 imprinted domain escape genomic imprinting. Lee MP, et al. Hum Mol Genet, 1999 Apr. PMID 10072438
    3. TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation. Klimešová K, et al. Nat Commun, 2021 Jun 15. PMID 34131137, Free PMC Article
    4. Sequence conservation and variability of imprinting in the Beckwith-Wiedemann syndrome gene cluster in human and mouse. Paulsen M, et al. Hum Mol Genet, 2000 Jul 22. PMID 10915772
    5. R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein. Cloutier P, et al. Nat Commun, 2017 May 31. PMID 28561026, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation.
      Title: TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation.
    2. TSSC4 gene, located in the center of the 11p15 imprinted region, escapes genomic imprinting.
      Title: Two novel genes in the center of the 11p15 imprinted domain escape genomic imprinting.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular sequestering activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in spliceosomal snRNP assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in spliceosomal tri-snRNP complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U5 snRNP IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    U5 small nuclear ribonucleoprotein TSSC4
    Names
    protein TSSC4
    tumor-suppressing STF cDNA 4 protein
    tumor-suppressing subchromosomal transferable fragment candidate gene 4 protein

    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_001297658.2 → NP_001284587.1  U5 small nuclear ribonucleoprotein TSSC4 isoform a

      See identical proteins and their annotated locations for NP_001284587.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AC124057, AF125568, BC006091, BC050616, BI768923
      Consensus CDS
      CCDS7735.1
      UniProtKB/Swiss-Prot
      C9JS66, Q86VL2, Q9BRS6, Q9Y5U2
      Conserved Domains (1) summary
      pfam15264
      Location:94 → 210
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    2. NM_001297659.2 → NP_001284588.1  U5 small nuclear ribonucleoprotein TSSC4 isoform a

      See identical proteins and their annotated locations for NP_001284588.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AC124057, AF125568, BC006091, BI084274
      Consensus CDS
      CCDS7735.1
      UniProtKB/Swiss-Prot
      C9JS66, Q86VL2, Q9BRS6, Q9Y5U2
      Conserved Domains (1) summary
      pfam15264
      Location:94 → 210
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    3. NM_001297660.2 → NP_001284589.1  U5 small nuclear ribonucleoprotein TSSC4 isoform a

      See identical proteins and their annotated locations for NP_001284589.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AC124057, AF125568, BC006091, BC050616, BX384913
      Consensus CDS
      CCDS7735.1
      UniProtKB/Swiss-Prot
      C9JS66, Q86VL2, Q9BRS6, Q9Y5U2
      Conserved Domains (1) summary
      pfam15264
      Location:94 → 210
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    4. NM_001297661.2 → NP_001284590.1  U5 small nuclear ribonucleoprotein TSSC4 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame segment compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC124057, BC050616
      Consensus CDS
      CCDS73241.1
      UniProtKB/Swiss-Prot
      Q9Y5U2
      Related
      ENSP00000370384.5, ENST00000380996.9
      Conserved Domains (1) summary
      pfam15264
      Location:30 → 146
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    5. NM_005706.4 → NP_005697.2  U5 small nuclear ribonucleoprotein TSSC4 isoform a

      See identical proteins and their annotated locations for NP_005697.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AC124057, AF125568, BC006091, BC050616
      Consensus CDS
      CCDS7735.1
      UniProtKB/Swiss-Prot
      C9JS66, Q86VL2, Q9BRS6, Q9Y5U2
      Related
      ENSP00000331087.6, ENST00000333256.11
      Conserved Domains (1) summary
      pfam15264
      Location:94 → 210
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      2400750..2403876
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006718118.3 → XP_006718181.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X1

      See identical proteins and their annotated locations for XP_006718181.1

      UniProtKB/Swiss-Prot
      C9JS66, Q86VL2, Q9BRS6, Q9Y5U2
      Conserved Domains (1) summary
      pfam15264
      Location:94 → 210
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    2. XM_047426216.1 → XP_047282172.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X2

    3. XM_047426218.1 → XP_047282174.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X2

    4. XM_011519830.4 → XP_011518132.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X1

      See identical proteins and their annotated locations for XP_011518132.1

      UniProtKB/Swiss-Prot
      C9JS66, Q86VL2, Q9BRS6, Q9Y5U2
      Conserved Domains (1) summary
      pfam15264
      Location:94 → 210
      TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

    5. XM_047426217.1 → XP_047282173.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      2490101..2493227
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367416.1 → XP_054223391.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X2

    2. XM_054367414.1 → XP_054223389.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X1

    3. XM_054367415.1 → XP_054223390.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5U2.3 GenPept UniProtKB/Swiss-Prot:Q9Y5U2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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