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

Gene ID: 10078, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (2400750..2403876)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (2490101..2493227)
105.20220307 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
  • 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 (35) 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_2023_10

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

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