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CLIP1 CAP-Gly domain containing linker protein 1 [ Homo sapiens (human) ]

Gene ID: 6249, updated on 7-Apr-2024

Summary

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Official Symbol
CLIP1provided by HGNC
Official Full Name
CAP-Gly domain containing linker protein 1provided by HGNC
Primary source
HGNC:HGNC:10461
See related
Ensembl:ENSG00000130779 MIM:179838; AllianceGenome:HGNC:10461
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
RSN; CLIP; CYLN1; CLIP170; CLIP-170
Summary
The protein encoded by this gene links endocytic vesicles to microtubules. This gene is highly expressed in Reed-Sternberg cells of Hodgkin disease. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in thyroid (RPKM 36.8), esophagus (RPKM 33.7) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
12q24.31
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (122271469..122422956, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122267259..122418870, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122756016..122907216, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2179 Neighboring gene uncharacterized LOC128125816 Neighboring gene uncharacterized LOC101593348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122711745-122712576 Neighboring gene diablo IAP-binding mitochondrial protein Neighboring gene VPS33A core subunit of CORVET and HOPS complexes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122750160-122751042 Neighboring gene MPRA-validated peak2017 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr12:122773535-122773694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7214 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122797254-122797754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122797755-122798255 Neighboring gene coiled-coil domain containing 150 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 10749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122869287-122869920 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:122870555-122871186 Neighboring gene ribosomal protein L21 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122885121-122885806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122885807-122886492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7219 Neighboring gene CLIP1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7221 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122916171-122916672 Neighboring gene Sharpr-MPRA regulatory region 9757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122927953-122928453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7226 Neighboring gene zinc finger CCHC-type containing 8 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122984447-122985138 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122985139-122985832 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122985833-122986524 Neighboring gene MPRA-validated peak2019 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7230 Neighboring gene arginine and serine rich coiled-coil 2

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. CLIP-170S is a microtubule +TIP variant that confers resistance to taxanes by impairing drug-target engagement. Thakkar PV, et al. Dev Cell, 2021 Dec 6. PMID 34672971, Free PMC Article
  2. CLIP-170 spatially modulates receptor tyrosine kinase recycling to coordinate cell migration. Zaoui K, et al. Traffic, 2019 Mar. PMID 30537020, Free PMC Article
  3. CLIP-170 is essential for MTOC repositioning during T cell activation by regulating dynein localisation on the cell surface. Lim WM, et al. Sci Rep, 2018 Nov 28. PMID 30487641, Free PMC Article
  4. Accelerated actin filament polymerization from microtubule plus ends. Henty-Ridilla JL, et al. Science, 2016 May 20. PMID 27199431, Free PMC Article
  5. Microtubule plus end-associated CLIP-170 initiates HSV-1 retrograde transport in primary human cells. Jovasevic V, et al. J Cell Biol, 2015 Oct 26. PMID 26504169, Free PMC Article

See all (112) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Restin protein expression in non-small cell lung cancer.
    Title: Restin protein expression in non-small cell lung cancer.
  2. The CLIP1-LTK fusion is an oncogenic driver in non-small-cell lung cancer.
    Title: The CLIP1-LTK fusion is an oncogenic driver in non-small-cell lung cancer.
  3. CLIP-170S is a microtubule +TIP variant that confers resistance to taxanes by impairing drug-target engagement.
    Title: CLIP-170S is a microtubule +TIP variant that confers resistance to taxanes by impairing drug-target engagement.
  4. SOCS3-microtubule interaction via CLIP-170 and CLASP2 is critical for modulation of endothelial inflammation and lung injury.
    Title: SOCS3-microtubule interaction via CLIP-170 and CLASP2 is critical for modulation of endothelial inflammation and lung injury.
  5. Stress-induced phosphorylation of CLIP-170 by JNK promotes microtubule rescue.
    Title: Stress-induced phosphorylation of CLIP-170 by JNK promotes microtubule rescue.
  6. CLIP-170 spatially modulates recycling of the Met RTK through direct binding of CLIP-170 to GGA3.
    Title: CLIP-170 spatially modulates receptor tyrosine kinase recycling to coordinate cell migration.
  7. CLIP-170 plays an indispensable role in MTOC repositioning and full activation of T cells by regulating dynein localisation.
    Title: CLIP-170 is essential for MTOC repositioning during T cell activation by regulating dynein localisation on the cell surface.
  8. Long noncoding RNA ANRIL regulates endothelial cell activities associated with coronary artery disease by up-regulating CLIP1, EZR, and LYVE1 genes
    Title: Long noncoding RNA ANRIL regulates endothelial cell activities associated with coronary artery disease by up-regulating CLIP1, EZR, and LYVE1 genes.
  9. finding that CLIP-170 has multiple non-CAP-Gly EB1-binding modules may explain why autoinhibition of CLIP-170 GAP-Gly domains does not fully abrogate its microtubule plus-end localization. This work expands our understanding of EB1-binding motifs and their multivalent networks.
    Title: Mapping multivalency in the CLIP-170-EB1 microtubule plus-end complex.
  10. we report an unexpected finding that CLIP170 negatively regulates TLR4 signaling by the targeted ubiquitination and degradation of TIRAP. Furthermore, we observed that CLIP170 expression is modulated by LPS to maintain the cellular homeostasis.
    Title: Cytoplasmic Linker Protein CLIP170 Negatively Regulates TLR4 Signaling by Targeting the TLR Adaptor Protein TIRAP.
Submit: New GeneRIF Correction See all GeneRIFs (47)

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

  • MGC131604

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables microtubule binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables microtubule plus-end binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables microtubule plus-end binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tubulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cytoplasmic microtubule organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in microtubule bundle formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitotic cell cycle TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of microtubule polymerization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of microtubule polymerization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cell cortex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in intermediate filament TAS
Traceable Author Statement
more info
 PubMed 
located_in kinetochore TAS
Traceable Author Statement
more info
 PubMed 
colocalizes_with macropinosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in microtubule IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in microtubule ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in microtubule cytoskeleton IMP
Inferred from Mutant Phenotype
more info
 PubMed 
colocalizes_with microtubule plus-end IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ruffle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
CAP-Gly domain-containing linker protein 1
Names
cytoplasmic linker protein 1
cytoplasmic linker protein 170 alpha-2
cytoplasmic linker protein CLIP-170
restin (Reed-Steinberg cell-expressed intermediate filament-associated 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.

Genomic

  1. NG_030352.1 RefSeqGene

    Range
    4901..156101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001247997.2 → NP_001234926.1  CAP-Gly domain-containing linker protein 1 isoform c

    See identical proteins and their annotated locations for NP_001234926.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
    Source sequence(s)
    AC048338, AC127002, BC126305, CB305431, M97501
    Consensus CDS
    CCDS58285.1
    UniProtKB/Swiss-Prot
    A0AVD3, P30622, Q17RS4, Q29RG0
    UniProtKB/TrEMBL
    J3KP58
    Related
    ENSP00000479322.1, ENST00000620786.5
    Conserved Domains (5) summary
    COG5244
    Location:212 → 812
    NIP100; Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell cycle control, cell division, chromosome partitioning]
    pfam01302
    Location:215 → 278
    CAP_GLY; CAP-Gly domain
    pfam07851
    Location:567 → 666
    TMPIT; TMPIT-like protein
    pfam10174
    Location:474 → 1255
    Cast; RIM-binding protein of the cytomatrix active zone
    pfam16641
    Location:1416 → 1432
    CLIP1_ZNF; CLIP1 zinc knuckle

  2. NM_001389291.1 → NP_001376220.1  CAP-Gly domain-containing linker protein 1 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC048338, AC079406, AC127002
    Conserved Domains (4) summary
    COG0419
    Location:335 → 835
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    COG1196
    Location:612 → 1442
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam01302
    Location:214 → 278
    CAP_GLY; CAP-Gly domain
    pfam16641
    Location:2126 → 2142
    CLIP1_ZNF; CLIP1 zinc knuckle

  3. NM_002956.3 → NP_002947.1  CAP-Gly domain-containing linker protein 1 isoform a

    See identical proteins and their annotated locations for NP_002947.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (a) has the same N- and C-termini but is shorter compared to isoform c.
    Source sequence(s)
    AC127002, AK126990, M97501, X64838
    Consensus CDS
    CCDS9232.1
    UniProtKB/TrEMBL
    J3KP58
    Related
    ENSP00000351665.2, ENST00000358808.6
    Conserved Domains (4) summary
    TIGR04523
    Location:429 → 1147
    Mplasa_alph_rch; helix-rich Mycoplasma protein
    pfam01302
    Location:215 → 278
    CAP_GLY; CAP-Gly domain
    pfam07851
    Location:556 → 655
    TMPIT; TMPIT-like protein
    pfam16641
    Location:1405 → 1421
    CLIP1_ZNF; CLIP1 zinc knuckle

  4. NM_198240.3 → NP_937883.1  CAP-Gly domain-containing linker protein 1 isoform b

    See identical proteins and their annotated locations for NP_937883.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two consecutive alternate in-frame exons compared to variant 3. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform c.
    Source sequence(s)
    AC127002, AK126990, BM998166, M97501, X64838
    Consensus CDS
    CCDS9233.1
    UniProtKB/TrEMBL
    J3KP58
    Related
    ENSP00000445531.1, ENST00000537178.5
    Conserved Domains (5) summary
    COG1196
    Location:609 → 1250
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    COG5244
    Location:212 → 866
    NIP100; Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell cycle control, cell division, chromosome partitioning]
    pfam01302
    Location:215 → 278
    CAP_GLY; CAP-Gly domain
    pfam07851
    Location:521 → 620
    TMPIT; TMPIT-like protein
    pfam16641
    Location:1370 → 1386
    CLIP1_ZNF; CLIP1 zinc knuckle

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    122271469..122422956 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429314.1 → XP_047285270.1  CAP-Gly domain-containing linker protein 1 isoform X6

  2. XM_047429321.1 → XP_047285277.1  CAP-Gly domain-containing linker protein 1 isoform X13

  3. XM_047429320.1 → XP_047285276.1  CAP-Gly domain-containing linker protein 1 isoform X12

  4. XM_047429318.1 → XP_047285274.1  CAP-Gly domain-containing linker protein 1 isoform X9

  5. XM_047429319.1 → XP_047285275.1  CAP-Gly domain-containing linker protein 1 isoform X11

  6. XM_017019792.3 → XP_016875281.1  CAP-Gly domain-containing linker protein 1 isoform X10

    UniProtKB/TrEMBL
    J3KP58

  7. XM_017019788.3 → XP_016875277.1  CAP-Gly domain-containing linker protein 1 isoform X6

    UniProtKB/TrEMBL
    J3KP58

  8. XM_017019791.3 → XP_016875280.1  CAP-Gly domain-containing linker protein 1 isoform X8

    UniProtKB/TrEMBL
    J3KP58

  9. XM_006719552.5 → XP_006719615.1  CAP-Gly domain-containing linker protein 1 isoform X2

    UniProtKB/TrEMBL
    J3KP58
    Conserved Domains (4) summary
    TIGR04523
    Location:429 → 1147
    Mplasa_alph_rch; helix-rich Mycoplasma protein
    pfam01302
    Location:215 → 278
    CAP_GLY; CAP-Gly domain
    pfam07851
    Location:556 → 655
    TMPIT; TMPIT-like protein
    pfam16641
    Location:1407 → 1423
    CLIP1_ZNF; CLIP1 zinc knuckle

  10. XM_047429313.1 → XP_047285269.1  CAP-Gly domain-containing linker protein 1 isoform X5

  11. XM_047429312.1 → XP_047285268.1  CAP-Gly domain-containing linker protein 1 isoform X4

  12. XM_005253593.4 → XP_005253650.1  CAP-Gly domain-containing linker protein 1 isoform X1

    UniProtKB/TrEMBL
    J3KP58
    Conserved Domains (5) summary
    COG5244
    Location:212 → 812
    NIP100; Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell cycle control, cell division, chromosome partitioning]
    pfam01302
    Location:215 → 278
    CAP_GLY; CAP-Gly domain
    pfam07851
    Location:567 → 666
    TMPIT; TMPIT-like protein
    pfam10174
    Location:474 → 1255
    Cast; RIM-binding protein of the cytomatrix active zone
    pfam16641
    Location:1418 → 1434
    CLIP1_ZNF; CLIP1 zinc knuckle

  13. XM_047429317.1 → XP_047285273.1  CAP-Gly domain-containing linker protein 1 isoform X7

  14. XM_047429315.1 → XP_047285271.1  CAP-Gly domain-containing linker protein 1 isoform X6

  15. XM_047429311.1 → XP_047285267.1  CAP-Gly domain-containing linker protein 1 isoform X4

  16. XM_047429307.1 → XP_047285263.1  CAP-Gly domain-containing linker protein 1 isoform X1

  17. XM_047429316.1 → XP_047285272.1  CAP-Gly domain-containing linker protein 1 isoform X7

  18. XM_017019789.2 → XP_016875278.1  CAP-Gly domain-containing linker protein 1 isoform X6

    UniProtKB/TrEMBL
    J3KP58

  19. XM_047429310.1 → XP_047285266.1  CAP-Gly domain-containing linker protein 1 isoform X3

  20. XM_047429309.1 → XP_047285265.1  CAP-Gly domain-containing linker protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    122267259..122418870 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372847.1 → XP_054228822.1  CAP-Gly domain-containing linker protein 1 isoform X6

  2. XM_054372856.1 → XP_054228831.1  CAP-Gly domain-containing linker protein 1 isoform X13

  3. XM_054372855.1 → XP_054228830.1  CAP-Gly domain-containing linker protein 1 isoform X12

  4. XM_054372852.1 → XP_054228827.1  CAP-Gly domain-containing linker protein 1 isoform X9

  5. XM_054372854.1 → XP_054228829.1  CAP-Gly domain-containing linker protein 1 isoform X11

  6. XM_054372853.1 → XP_054228828.1  CAP-Gly domain-containing linker protein 1 isoform X10

  7. XM_054372845.1 → XP_054228820.1  CAP-Gly domain-containing linker protein 1 isoform X6

  8. XM_054372851.1 → XP_054228826.1  CAP-Gly domain-containing linker protein 1 isoform X8

  9. XM_054372839.1 → XP_054228814.1  CAP-Gly domain-containing linker protein 1 isoform X2

  10. XM_054372844.1 → XP_054228819.1  CAP-Gly domain-containing linker protein 1 isoform X5

  11. XM_054372843.1 → XP_054228818.1  CAP-Gly domain-containing linker protein 1 isoform X4

  12. XM_054372837.1 → XP_054228812.1  CAP-Gly domain-containing linker protein 1 isoform X1

  13. XM_054372838.1 → XP_054228813.1  CAP-Gly domain-containing linker protein 1 isoform X1

  14. XM_054372840.1 → XP_054228815.1  CAP-Gly domain-containing linker protein 1 isoform X2

  15. XM_054372842.1 → XP_054228817.1  CAP-Gly domain-containing linker protein 1 isoform X4

  16. XM_054372841.1 → XP_054228816.1  CAP-Gly domain-containing linker protein 1 isoform X3

  17. XM_054372848.1 → XP_054228823.1  CAP-Gly domain-containing linker protein 1 isoform X6

  18. XM_054372846.1 → XP_054228821.1  CAP-Gly domain-containing linker protein 1 isoform X6

  19. XM_054372850.1 → XP_054228825.1  CAP-Gly domain-containing linker protein 1 isoform X7

  20. XM_054372849.1 → XP_054228824.1  CAP-Gly domain-containing linker protein 1 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P30622.2 GenPept UniProtKB/Swiss-Prot:P30622

Gene LinkOut

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