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    CLIP3 CAP-Gly domain containing linker protein 3 [ Homo sapiens (human) ]

    Gene ID: 25999, updated on 17-Jun-2024

    Summary

    Official Symbol
    CLIP3provided by HGNC
    Official Full Name
    CAP-Gly domain containing linker protein 3provided by HGNC
    Primary source
    HGNC:HGNC:24314
    See related
    Ensembl:ENSG00000105270 MIM:607382; AllianceGenome:HGNC:24314
    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
    Also known as
    RSNL1; CLIPR59; CLIPR-59
    Summary
    This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
    Expression
    Biased expression in brain (RPKM 97.6), endometrium (RPKM 19.6) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CLIP3 in Genome Data Viewer
    Location:
    19q13.12
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (36014660..36032873, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38560459..38578672, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36505562..36523775, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36498887-36499428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36499429-36499968 Neighboring gene spectrin repeat containing nuclear envelope family member 4 Neighboring gene uncharacterized LOC101927572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14514 Neighboring gene alkB homolog 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36526501-36526674 Neighboring gene THAP domain containing 8 Neighboring gene RNY5 pseudogene 10 Neighboring gene WD repeat domain 62 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36591509-36592010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36601644-36602274 Neighboring gene ovo like zinc finger 3

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of CAP-GLY domain containing linker protein 3 (CLIP3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ33413, DKFZp586N1922

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ganglioside binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables microtubule binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables microtubule binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables microtubule plus-end binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi stack IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cell cortex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in microtubule plus-end IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in trans-Golgi network membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in trans-Golgi network membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    CAP-Gly domain-containing linker protein 3
    Names
    CLIP-170-related 59 kDa protein
    cytoplasmic linker protein 170-related 59 kDa protein
    restin-like 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001199570.2NP_001186499.1  CAP-Gly domain-containing linker protein 3

      See identical proteins and their annotated locations for NP_001186499.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK289509, AL117468
      Consensus CDS
      CCDS12486.1
      UniProtKB/Swiss-Prot
      A8K0E4, Q8WWL1, Q96C99, Q96DZ5, Q9UFT7
      UniProtKB/TrEMBL
      B4DGS7
      Related
      ENSP00000466832.1, ENST00000593074.5
      Conserved Domains (3) summary
      sd00045
      Location:120157
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:418482
      CAP_GLY; CAP-Gly domain
      pfam12796
      Location:122228
      Ank_2; Ankyrin repeats (3 copies)
    2. NM_015526.3NP_056341.1  CAP-Gly domain-containing linker protein 3

      See identical proteins and their annotated locations for NP_056341.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AJ427922, AL117468
      Consensus CDS
      CCDS12486.1
      UniProtKB/Swiss-Prot
      A8K0E4, Q8WWL1, Q96C99, Q96DZ5, Q9UFT7
      UniProtKB/TrEMBL
      B4DGS7
      Related
      ENSP00000353732.3, ENST00000360535.9
      Conserved Domains (3) summary
      sd00045
      Location:120157
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:418482
      CAP_GLY; CAP-Gly domain
      pfam12796
      Location:122228
      Ank_2; Ankyrin repeats (3 copies)

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      36014660..36032873 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      38560459..38578672 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)