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

    Gene ID: 6249, updated on 28-Oct-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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    See CLIP1 in Genome Data Viewer
    Location:
    12q24.31
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (122271469..122422956, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122267259..122418870, complement)
    RS_2024_09 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 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. Regulation of lamellipodia formation and cell invasion by CLIP-170 in invasive human breast cancer cells. Suzuki K, et al. Biochem Biophys Res Commun, 2008 Apr 4. PMID 18237546
    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 (120) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CLIP170 inhibits the metastasis and EMT of papillary thyroid cancer through the TGF-beta pathway.
      Title: CLIP170 inhibits the metastasis and EMT of papillary thyroid cancer through the TGF-β pathway.
    2. Restin protein expression in non-small cell lung cancer.
      Title: Restin protein expression in non-small cell lung cancer.
    3. 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.
    4. 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.
    5. 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.
    6. Stress-induced phosphorylation of CLIP-170 by JNK promotes microtubule rescue.
      Title: Stress-induced phosphorylation of CLIP-170 by JNK promotes microtubule rescue.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (48)

    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 plasma membrane TAS
    Traceable Author Statement
    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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    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.

    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_2024_08

    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

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