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    CLASRP CLK4 associating serine/arginine rich protein [ Homo sapiens (human) ]

    Gene ID: 11129, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CLASRPprovided by HGNC
    Official Full Name
    CLK4 associating serine/arginine rich proteinprovided by HGNC
    Primary source
    HGNC:HGNC:17731
    See related
    Ensembl:ENSG00000104859 MIM:618532; AllianceGenome:HGNC:17731
    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
    Also known as
    CLASP; SWAP2; SFRS16
    Summary
    Predicted to be involved in RNA splicing and mRNA processing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 17.9), spleen (RPKM 17.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLASRP in Genome Data Viewer
    Location:
    19q13.32
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45039045..45070956)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (47864144..47896071)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (45542303..45574214)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10745 Neighboring gene MPRA-validated peak3513 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14775 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:45464990-45465143 Neighboring gene CLPTM1 regulator of GABA type A receptor forward trafficking Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10747 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10748 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:45514891-45515392 Neighboring gene RELB proto-oncogene, NF-kB subunit Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10749 Neighboring gene Sharpr-MPRA regulatory region 3318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45541977-45542846 Neighboring gene Sharpr-MPRA regulatory region 2438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45552602-45553156 Neighboring gene RNA, U6 small nuclear 611, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10753 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:45582765-45583532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45584301-45585066 Neighboring gene zinc finger protein 296 Neighboring gene gem nuclear organelle associated protein 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:45593049-45594044 Neighboring gene GEMIN7 antisense RNA 1

    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. A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts. Xu Z, et al. Clin Epigenetics, 2019 Mar 4. PMID 30832715, Free PMC Article
    2. Novel SR-rich-related protein clasp specifically interacts with inactivated Clk4 and induces the exon EB inclusion of Clk. Katsu R, et al. J Biol Chem, 2002 Nov 15. PMID 12169693
    3. Characterization of cyclin L2, a novel cyclin with an arginine/serine-rich domain: phosphorylation by DYRK1A and colocalization with splicing factors. de Graaf K, et al. J Biol Chem, 2004 Feb 6. PMID 14623875
    4. Identification and characterization of essential genes in the human genome. Wang T, et al. Science, 2015 Nov 27. PMID 26472758, Free PMC Article
    5. Ubiquitin-like protein 3 (UBL3) is required for MARCH ubiquitination of major histocompatibility complex class II and CD86. Liu H, et al. Nat Commun, 2022 Apr 11. PMID 35411049, Free PMC Article

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data identified a significantly differentially methylated cg26985354 near gene CLASRP to be associated with cleft lip and cleft palate.
      Title: A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ90109

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    CLK4-associating serine/arginine rich protein
    Names
    Clk4 associating SR-related protein
    splicing factor, arginine/serine-rich 16 (suppressor-of-white-apricot homolog, Drosophila)
    suppressor of white apricot homolog 2

    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_001278439.2 → NP_001265368.1  CLK4-associating serine/arginine rich protein isoform 2

      See identical proteins and their annotated locations for NP_001265368.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame segment compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AF042800, AK293333
      Consensus CDS
      CCDS62710.1
      UniProtKB/TrEMBL
      F5H0Q6
      Related
      ENSP00000375815.3, ENST00000391953.8
      Conserved Domains (1) summary
      pfam09750
      Location:43 → 107
      DRY_EERY; Alternative splicing regulator

    2. NM_007056.3 → NP_008987.2  CLK4-associating serine/arginine rich protein isoform 1

      See identical proteins and their annotated locations for NP_008987.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AF042800
      Consensus CDS
      CCDS12652.2
      UniProtKB/Swiss-Prot
      A0A0A0MQS2, B4DDT8, F8WAG9, O96026, Q6UW71, Q8N2M8, Q96DX2
      UniProtKB/TrEMBL
      F5H0Q6
      Related
      ENSP00000221455.3, ENST00000221455.8
      Conserved Domains (1) summary
      pfam09750
      Location:41 → 169
      DRY_EERY; Alternative splicing regulator

    RNA

    1. NR_103529.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction at the 3' end of an exon compared to variant 1, that causes a frameshift. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF042800, AY358944

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      45039045..45070956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011526396.2 → XP_011524698.1  CLK4-associating serine/arginine rich protein isoform X1

      UniProtKB/TrEMBL
      B3KSZ8
      Conserved Domains (1) summary
      pfam09750
      Location:41 → 169
      DRY_EERY; Alternative splicing regulator

    2. XM_047438116.1 → XP_047294072.1  CLK4-associating serine/arginine rich protein isoform X2

      Related
      ENSP00000375814.2, ENST00000391952.7

    3. XM_011526397.4 → XP_011524699.1  CLK4-associating serine/arginine rich protein isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      47864144..47896071
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319671.1 → XP_054175646.1  CLK4-associating serine/arginine rich protein isoform X1

    2. XM_054319672.1 → XP_054175647.1  CLK4-associating serine/arginine rich protein isoform X2

    3. XM_054319673.1 → XP_054175648.1  CLK4-associating serine/arginine rich protein isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N2M8.5 GenPept UniProtKB/Swiss-Prot:Q8N2M8

    Gene LinkOut

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

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