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    CLIP4 CAP-Gly domain containing linker protein family member 4 [ Homo sapiens (human) ]

    Gene ID: 79745, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CLIP4provided by HGNC
    Official Full Name
    CAP-Gly domain containing linker protein family member 4provided by HGNC
    Primary source
    HGNC:HGNC:26108
    See related
    Ensembl:ENSG00000115295 AllianceGenome:HGNC:26108
    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
    RSNL2
    Summary
    Predicted to enable microtubule plus-end binding activity. Predicted to be involved in cytoplasmic microtubule organization. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 10.8), skin (RPKM 7.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLIP4 in Genome Data Viewer
    Location:
    2p23.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (29097726..29183808)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (29141179..29227263)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (29320592..29406674)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15529 Neighboring gene TOG array regulator of axonemal microtubules 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:29246593-29247094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:29264781-29265402 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:29275821-29276331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:29285737-29286651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:29287995-29288677 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:29289979-29290479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:29303580-29304080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15531 Neighboring gene uncharacterized LOC105374386 Neighboring gene CLIP4 5' region CAGE-defined mid-level expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11319 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11320 Neighboring gene uncharacterized LOC124907747 Neighboring gene photoreceptor cilium actin regulator Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:29474025-29474526 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:29474527-29475026 Neighboring gene ALK receptor tyrosine kinase Neighboring gene uncharacterized LOC101929386 Neighboring gene Sharpr-MPRA regulatory region 127 Neighboring gene uncharacterized LOC105374389

    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. FOXC2 and CLIP4 : a potential biomarker for synchronous metastasis of ≤7-cm clear cell renal cell carcinomas. Ahn J, et al. Oncotarget, 2016 Aug 9. PMID 27283491, Free PMC Article
    2. miR-135b-5p promotes gastric carcinogenesis by targeting CLIP4-mediated JAK2/STAT3 signal pathway. Peng Z, et al. Cell Signal, 2024 Oct. PMID 39121973
    3. A Novel GLP1 Receptor Interacting Protein ATP6ap2 Regulates Insulin Secretion in Pancreatic Beta Cells. Dai FF, et al. J Biol Chem, 2015 Oct 9. PMID 26272612, Free PMC Article
    4. rec-YnH enables simultaneous many-by-many detection of direct protein-protein and protein-RNA interactions. Yang JS, et al. Nat Commun, 2018 Sep 14. PMID 30217970, Free PMC Article
    5. The CRL4(DCAF6) E3 ligase ubiquitinates CtBP1/2 to induce apoptotic signalling and promote intervertebral disc degeneration. Tseng C, et al. J Mol Med (Berl), 2023 Feb. PMID 36688959

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. miR-135b-5p promotes gastric carcinogenesis by targeting CLIP4-mediated JAK2/STAT3 signal pathway.
      Title: miR-135b-5p promotes gastric carcinogenesis by targeting CLIP4-mediated JAK2/STAT3 signal pathway.
    2. FOXC2 and CLIP4 activity correlates to the presence of </=7-cm clear cell renal cell carcinomas (ccRCCs) with synchronous metastasis and may be potential molecular predictors of synchronous metastasis of </=7-cm ccRCCs.
      Title: FOXC2 and CLIP4 : a potential biomarker for synchronous metastasis of ≤7-cm clear cell renal cell carcinomas.
    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

    Clone Names

    • FLJ21069, FLJ32705

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 
    Process Evidence Code Pubs
    involved_in cytoplasmic microtubule organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell cortex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    CAP-Gly domain-containing linker protein 4
    Names
    CAP-GLY domain containing linker protein family, member 4
    restin-like protein 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_001287527.2 → NP_001274456.1  CAP-Gly domain-containing linker protein 4 isoform 1

      See identical proteins and their annotated locations for NP_001274456.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AC105398, AK023505, AK304384, AL834443, BI600762
      Consensus CDS
      CCDS1770.1
      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0
      UniProtKB/TrEMBL
      A8K6D0
      Related
      ENSP00000509159.1, ENST00000693264.1
      Conserved Domains (3) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:487 → 551
      CAP_GLY; CAP-Gly domain

    2. NM_001287528.2 → NP_001274457.1  CAP-Gly domain-containing linker protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001274457.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, and its 3'-terminal exon extends past a splice site that is used in variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AA429893, AF433661, AK291595, AK302325, DC317668
      Consensus CDS
      CCDS74502.1
      UniProtKB/TrEMBL
      A0A8I5KUB8
      Related
      ENSP00000384242.1, ENST00000401605.5
      Conserved Domains (4) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      pfam01302
      Location:488 → 551
      CAP_GLY; CAP-Gly domain
      pfam12796
      Location:111 → 217
      Ank_2; Ankyrin repeats (3 copies)
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]

    3. NM_001410747.1 → NP_001397676.1  CAP-Gly domain-containing linker protein 4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC093593, AC105398
      Consensus CDS
      CCDS92728.1
      UniProtKB/TrEMBL
      A0A8I5QKV0
      Related
      ENSP00000509643.1, ENST00000689070.1

    4. NM_024692.6 → NP_078968.3  CAP-Gly domain-containing linker protein 4 isoform 1

      See identical proteins and their annotated locations for NP_078968.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AC105398, AK023505, AK304384, AL834443, BI600762
      Consensus CDS
      CCDS1770.1
      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0
      UniProtKB/TrEMBL
      A8K6D0
      Related
      ENSP00000327009.5, ENST00000320081.10
      Conserved Domains (3) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:487 → 551
      CAP_GLY; CAP-Gly domain

    RNA

    1. NR_109844.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses alternate 5' and 3'-terminal exons, lacks an internal exon, and uses an alternate splice site at an internal exon, compared to variant 1. 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)
      AA429893, AK057267, AL834443
      Related
      ENST00000456385.5

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      29097726..29183808
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005264562.3 → XP_005264619.1  CAP-Gly domain-containing linker protein 4 isoform X1

      See identical proteins and their annotated locations for XP_005264619.1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0
      UniProtKB/TrEMBL
      A8K6D0
      Conserved Domains (3) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:487 → 551
      CAP_GLY; CAP-Gly domain

    2. XM_011533110.2 → XP_011531412.1  CAP-Gly domain-containing linker protein 4 isoform X4

      UniProtKB/TrEMBL
      A0A8I5KXU9, Q4ZFY2
      Related
      ENSP00000508721.1, ENST00000687104.1
      Conserved Domains (4) summary
      cd00204
      Location:1 → 145
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      pfam01302
      Location:381 → 444
      CAP_GLY; CAP-Gly domain
      pfam12796
      Location:4 → 110
      Ank_2; Ankyrin repeats (3 copies)
      sd00045
      Location:46 → 77
      ANK; ANK repeat [structural motif]

    3. XM_005264563.2 → XP_005264620.1  CAP-Gly domain-containing linker protein 4 isoform X1

      See identical proteins and their annotated locations for XP_005264620.1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0
      UniProtKB/TrEMBL
      A8K6D0
      Conserved Domains (3) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:487 → 551
      CAP_GLY; CAP-Gly domain

    4. XM_006712104.3 → XP_006712167.1  CAP-Gly domain-containing linker protein 4 isoform X1

      See identical proteins and their annotated locations for XP_006712167.1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0
      UniProtKB/TrEMBL
      A8K6D0
      Related
      ENSP00000385594.1, ENST00000404424.5
      Conserved Domains (3) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:487 → 551
      CAP_GLY; CAP-Gly domain

    5. XM_047445849.1 → XP_047301805.1  CAP-Gly domain-containing linker protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8I5QKP4
      Related
      ENSP00000509057.1, ENST00000686125.1

    6. XM_011533109.2 → XP_011531411.1  CAP-Gly domain-containing linker protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011531411.1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0
      UniProtKB/TrEMBL
      A8K6D0
      Conserved Domains (3) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:487 → 551
      CAP_GLY; CAP-Gly domain

    7. XM_017004958.2 → XP_016860447.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0
      UniProtKB/TrEMBL
      A8K6D0
      Related
      ENSP00000508552.1, ENST00000690063.1
      Conserved Domains (3) summary
      cd00204
      Location:98 → 252
      ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
      sd00045
      Location:153 → 184
      ANK; ANK repeat [structural motif]
      pfam01302
      Location:487 → 551
      CAP_GLY; CAP-Gly domain

    8. XM_017004959.3 → XP_016860448.1  CAP-Gly domain-containing linker protein 4 isoform X3

      UniProtKB/TrEMBL
      A0A8I5KUB8

    9. XM_047445851.1 → XP_047301807.1  CAP-Gly domain-containing linker protein 4 isoform X5

      UniProtKB/TrEMBL
      G3XAK3
      Related
      ENSP00000414417.1, ENST00000415891.5

    10. XM_047445848.1 → XP_047301804.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0

    11. XM_047445850.1 → XP_047301806.1  CAP-Gly domain-containing linker protein 4 isoform X4

      UniProtKB/TrEMBL
      A0A8I5KXU9
      Related
      ENSP00000509274.1, ENST00000691796.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      29141179..29227263
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343950.1 → XP_054199925.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0

    2. XM_054343954.1 → XP_054199929.1  CAP-Gly domain-containing linker protein 4 isoform X4

      UniProtKB/TrEMBL
      A0A8I5KXU9

    3. XM_054343946.1 → XP_054199921.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0

    4. XM_054343947.1 → XP_054199922.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0

    5. XM_054343952.1 → XP_054199927.1  CAP-Gly domain-containing linker protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8I5QKP4

    6. XM_054343948.1 → XP_054199923.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0

    7. XM_054343951.1 → XP_054199926.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0

    8. XM_054343953.1 → XP_054199928.1  CAP-Gly domain-containing linker protein 4 isoform X3

    9. XM_054343956.1 → XP_054199931.1  CAP-Gly domain-containing linker protein 4 isoform X5

      UniProtKB/TrEMBL
      G3XAK3

    10. XM_054343949.1 → XP_054199924.1  CAP-Gly domain-containing linker protein 4 isoform X1

      UniProtKB/Swiss-Prot
      A0AV10, B2RMQ3, B7Z7N8, Q7Z4U3, Q8N3C7, Q96BR7, Q96MA5, Q9H7C0

    11. XM_054343955.1 → XP_054199930.1  CAP-Gly domain-containing linker protein 4 isoform X4

      UniProtKB/TrEMBL
      A0A8I5KXU9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N3C7.1 GenPept UniProtKB/Swiss-Prot:Q8N3C7

    Gene LinkOut

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