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Tssc4 tumor-suppressing subchromosomal transferable fragment 4 [ Mus musculus (house mouse) ]

Gene ID: 56844, updated on 5-Mar-2024

Summary

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Official Symbol
Tssc4provided by MGI
Official Full Name
tumor-suppressing subchromosomal transferable fragment 4provided by MGI
Primary source
MGI:MGI:1861712
See related
Ensembl:ENSMUSG00000045752 AllianceGenome:MGI:1861712
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
ESTM671070
Summary
Is expressed in several structures, including extraembryonic component; gut; liver; placenta; and spleen. Orthologous to human TSSC4 (tumor suppressing subtransferable candidate 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary adult (RPKM 20.3), limb E14.5 (RPKM 20.3) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
7 F5; 7 88.11 cM
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (142621049..142624830)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (143068416..143071093)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E4987 Neighboring gene STARR-positive B cell enhancer ABC_E6616 Neighboring gene tetraspanin 32 Neighboring gene STARR-seq mESC enhancer starr_20520 Neighboring gene STARR-positive B cell enhancer ABC_E6617 Neighboring gene STARR-seq mESC enhancer starr_20521 Neighboring gene expressed sequence R74862 Neighboring gene nonconserved acetylation island sequence M93 enhancer Neighboring gene CD81 antigen Neighboring gene VISTA enhancer mm183 Neighboring gene transient receptor potential cation channel, subfamily M, member 5 Neighboring gene STARR-seq mESC enhancer starr_20525 Neighboring gene potassium voltage-gated channel, subfamily Q, member 1 Neighboring gene predicted gene 28821

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo. Lewis A, et al. Development, 2006 Nov. PMID 17021040
  2. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Mancini-Dinardo D, et al. Genes Dev, 2006 May 15. PMID 16702402, Free PMC Article
  3. The two-domain hypothesis in Beckwith-Wiedemann syndrome: autonomous imprinting of the telomeric domain of the distal chromosome 7 cluster. Cerrato F, et al. Hum Mol Genet, 2005 Feb 15. PMID 15640248
  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. Transcription factor ASCL2 is required for development of the glycogen trophoblast cell lineage. Bogutz AB, et al. PLoS Genet, 2018 Aug. PMID 30096149, Free PMC Article

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

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 MGI

Function Evidence Code Pubs
enables molecular sequestering activity ISO
Inferred from Sequence Orthology
more info
  
enables molecular_function ND
No biological Data available
more info
  
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in spliceosomal snRNP assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in spliceosomal tri-snRNP complex assembly ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of U5 snRNP ISO
Inferred from Sequence Orthology
more info
  
is_active_in cellular_component ND
No biological Data available
more info
  
is_active_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
  
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

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_001115085.1 → NP_001108557.1  U5 small nuclear ribonucleoprotein TSSC4 isoform 1

    See identical proteins and their annotated locations for NP_001108557.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 both encode the same isoform (1).
    Source sequence(s)
    AB038011, CX239537
    Consensus CDS
    CCDS40195.1
    UniProtKB/Swiss-Prot
    Q9JHE7
    Related
    ENSMUSP00000137399.2, ENSMUST00000177841.8
    Conserved Domains (1) summary
    pfam15264
    Location:91 → 207
    TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

  2. NM_020285.2 → NP_064681.1  U5 small nuclear ribonucleoprotein TSSC4 isoform 1

    See identical proteins and their annotated locations for NP_064681.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 3 both encode the same isoform.
    Source sequence(s)
    AB038011
    Consensus CDS
    CCDS40195.1
    UniProtKB/Swiss-Prot
    Q9JHE7
    Related
    ENSMUSP00000056582.4, ENSMUST00000060433.10
    Conserved Domains (1) summary
    pfam15264
    Location:91 → 207
    TSSC4; Tumour suppressing sub-chromosomal transferable candidate 4

  3. NM_138631.1 → NP_619537.1  U5 small nuclear ribonucleoprotein TSSC4 isoform 2

    See identical proteins and their annotated locations for NP_619537.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding segment compared to variant 1, that causes a frameshift. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AJ279797
    Consensus CDS
    CCDS40196.1
    UniProtKB/TrEMBL
    Q9JHE9
    Related
    ENSMUSP00000101540.2, ENSMUST00000105920.8
    Conserved Domains (1) summary
    pfam15264
    Location:91 → 112
    TSSC4; tumor suppressing sub-chromosomal transferable candidate 4

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    142621049..142624830
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017322385.3 → XP_017177874.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X1

    Conserved Domains (1) summary
    pfam15264
    Location:160 → 276
    TSSC4; tumor suppressing sub-chromosomal transferable candidate 4

  2. XM_030242821.2 → XP_030098681.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X3

    UniProtKB/TrEMBL
    Q9JHE9
    Related
    ENSMUSP00000146914.2, ENSMUST00000208779.2
    Conserved Domains (1) summary
    pfam15264
    Location:91 → 112
    TSSC4; tumor suppressing sub-chromosomal transferable candidate 4

  3. XM_006508648.5 → XP_006508711.1  U5 small nuclear ribonucleoprotein TSSC4 isoform X2

    Conserved Domains (1) summary
    pfam15264
    Location:160 → 181
    TSSC4; tumor suppressing sub-chromosomal transferable candidate 4
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9JHE7.1 GenPept UniProtKB/Swiss-Prot:Q9JHE7

Gene LinkOut

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