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    CARMIL1 capping protein regulator and myosin 1 linker 1 [ Homo sapiens (human) ]

    Gene ID: 55604, updated on 5-May-2024

    Summary

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    Official Symbol
    CARMIL1provided by HGNC
    Official Full Name
    capping protein regulator and myosin 1 linker 1provided by HGNC
    Primary source
    HGNC:HGNC:21581
    See related
    Ensembl:ENSG00000079691 MIM:609593; AllianceGenome:HGNC:21581
    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
    CARMIL; LRRC16; LRRC16A; CARMIL1a; dJ501N12.1; dJ501N12.5
    Summary
    Involved in several processes, including actin filament network formation; plasma membrane bounded cell projection organization; and positive regulation of cellular component organization. Located in several cellular components, including lamellipodium; macropinosome; and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 7.4), small intestine (RPKM 6.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    6p22.2
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (25279374..25620530)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (25145130..25486328)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (25279602..25620758)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928663 Neighboring gene katanin regulatory subunit B1 like 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16995 Neighboring gene ribosomal protein L21 pseudogene 68 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:25292659-25293159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:25311331-25311831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:25315887-25316577 Neighboring gene uncharacterized LOC124901281 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:25342051-25342783 Neighboring gene RNA, U6 small nuclear 987, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24169 Neighboring gene uncharacterized LOC124901546 Neighboring gene NANOG hESC enhancer GRCh37_chr6:25462672-25463208 Neighboring gene MPRA-validated peak5738 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:25504114-25505313 Neighboring gene MPRA-validated peak5739 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:25627151-25627701 Neighboring gene NANOG hESC enhancer GRCh37_chr6:25635867-25636368 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:25660432-25661631 Neighboring gene uncharacterized LOC124901284 Neighboring gene PRELID1 pseudogene 2 Neighboring gene secretagogin, EF-hand calcium binding protein

    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. Novel CARMIL2 Mutations in Patients with Variable Clinical Dermatitis, Infections, and Combined Immunodeficiency. Alazami AM, et al. Front Immunol, 2018. PMID 29479355, Free PMC Article
    2. A Missense Genetic Variant in LRRC16A/CARMIL1 Improves Acute Respiratory Distress Syndrome Survival by Attenuating Platelet Count Decline. Wei Y, et al. Am J Respir Crit Care Med, 2017 May 15. PMID 27768389, Free PMC Article
    3. Physiological role of the interaction between CARMIL1 and capping protein. Edwards M, et al. Mol Biol Cell, 2013 Oct. PMID 23904264, Free PMC Article
    4. Mechanism for CARMIL protein inhibition of heterodimeric actin-capping protein. Kim T, et al. J Biol Chem, 2012 May 4. PMID 22411988, Free PMC Article
    5. Allosteric Coupling of CARMIL and V-1 Binding to Capping Protein Revealed by Hydrogen-Deuterium Exchange. Johnson B, et al. Cell Rep, 2018 May 29. PMID 29847807, Free PMC Article

    See all (58) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Leucine-Rich Repeat Region of CARMIL1 Regulates IL-1-Mediated ERK Activation, MMP Expression, and Collagen Degradation.
      Title: The Leucine-Rich Repeat Region of CARMIL1 Regulates IL-1-Mediated ERK Activation, MMP Expression, and Collagen Degradation.
    2. V-1 and CARMIL induce changes in both proteins' binding sites on the surface of capping proteins, along with a set of internal residues.
      Title: Allosteric Coupling of CARMIL and V-1 Binding to Capping Protein Revealed by Hydrogen-Deuterium Exchange.
    3. Study utilized whole exome sequencing and other assays to genetically and functionally characterize three consanguineous multiplex Saudi families with CARMIL2 mutations, presenting with dermatitis, recurrent skin abscesses and chest infections.
      Title: Novel CARMIL2 Mutations in Patients with Variable Clinical Dermatitis, Infections, and Combined Immunodeficiency.
    4. A novel genetic variant in leucine-rich repeat-containing 16A (LRRC16A) has been associated with reduced ARDS risk.
      Title: A Missense Genetic Variant in LRRC16A/CARMIL1 Improves Acute Respiratory Distress Syndrome Survival by Attenuating Platelet Count Decline.
    5. LRRC16A plays a role in adult respiratory distress syndrome pathophysiology by interacting with, and being mediated through, platelets.
      Title: Platelet count mediates the contribution of a genetic variant in LRRC16A to ARDS risk.
    6. shown for the first time that CARMIL/LRRC16A was associated with gout, which could be due to urate transportsome failure
      Title: Common variant of leucine-rich repeat-containing 16A (LRRC16A) gene is associated with gout susceptibility.
    7. The results also suggest that the ability of CARMIL1 to inhibit CP in cells may be regulated.
      Title: Physiological role of the interaction between CARMIL1 and capping protein.
    8. Data suggest that CARMIL promotes uncapping by binding to a freely accessible site on Capping protein (CP) bound to a filament barbed end and inducing a change in the conformation of the actin-binding surface of CP.
      Title: Mechanism for CARMIL protein inhibition of heterodimeric actin-capping protein.
    9. The two CARMIL isoforms are both important for cell migration, but they have distinct functions.[CARMIL1, CARMIL2]
      Title: Distinct roles for CARMIL isoforms in cell migration.
    10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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

    EBI GWAS Catalog

    Description
    A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.
    EBI GWAS Catalog
    Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations.
    EBI GWAS Catalog
    New gene functions in megakaryopoiesis and platelet formation.
    EBI GWAS Catalog
    Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of leucine rich repeat containing 16A (LRRC16A) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ20048, FLJ43708

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin filament network formation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in actin filament organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in barbed-end actin filament uncapping ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lamellipodium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in macropinocytosis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of barbed-end actin filament capping ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of actin filament polymerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of lamellipodium organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of stress fiber assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of substrate adhesion-dependent cell spreading IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of Arp2/3 complex-mediated actin nucleation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ruffle organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in urate metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell leading edge IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    part_of filamentous actin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in lamellipodium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lamellipodium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in macropinosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    F-actin-uncapping protein LRRC16A
    Names
    CARMIL homolog
    capping protein regulator and myosin 1 linker protein 1
    capping protein, Arp2/3 and myosin-I linker homolog 1
    capping protein, Arp2/3 and myosin-I linker protein 1
    capping protein, Arp2/3, and Myosin-I Linker homolog 1
    leucine rich repeat containing 16
    leucine rich repeat containing 16A
    leucine-rich repeat-containing protein 16A
    testicular tissue protein Li 107

    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.

    mRNA and Protein(s)

    1. NM_001173977.2 → NP_001167448.1  F-actin-uncapping protein LRRC16A isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal 6-aa segment near the C-terminus, compared to isoform 1.
      Source sequence(s)
      AL022170, AL024509, AL160037
      Consensus CDS
      CCDS93871.1
      UniProtKB/TrEMBL
      A0A8V8TRE2, B2RTQ5
      Related
      ENSP00000515137.1, ENST00000700669.1
      Conserved Domains (4) summary
      cd00116
      Location:229 → 373
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:484 → 507
      LRR_RI; leucine-rich repeat [structural motif]
      sd00034
      Location:248 → 277
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam16000
      Location:786 → 1078
      CARMIL_C; CARMIL C-terminus

    2. NM_017640.6 → NP_060110.4  F-actin-uncapping protein LRRC16A isoform 1

      See identical proteins and their annotated locations for NP_060110.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL022170, AL024509, AL160037
      Consensus CDS
      CCDS54973.1
      UniProtKB/Swiss-Prot
      B8X1J0, Q5VZK9, Q6ZUH5, Q6ZW07, Q9NXU7
      UniProtKB/TrEMBL
      B2RTQ5
      Related
      ENSP00000331983.6, ENST00000329474.7
      Conserved Domains (4) summary
      cd00116
      Location:229 → 373
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:484 → 507
      LRR_RI; leucine-rich repeat [structural motif]
      sd00034
      Location:248 → 277
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam16000
      Location:786 → 1078
      CARMIL_C; CARMIL C-terminus

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      25279374..25620530
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011008.2 → XP_016866497.1  F-actin-uncapping protein LRRC16A isoform X1

      UniProtKB/TrEMBL
      B2RTQ5

    2. XM_017011009.2 → XP_016866498.1  F-actin-uncapping protein LRRC16A isoform X2

      UniProtKB/TrEMBL
      B2RTQ5

    3. XM_017011015.2 → XP_016866504.1  F-actin-uncapping protein LRRC16A isoform X12

      UniProtKB/TrEMBL
      B2RTQ5

    4. XM_017011012.2 → XP_016866501.1  F-actin-uncapping protein LRRC16A isoform X5

      UniProtKB/TrEMBL
      B2RTQ5

    5. XM_024446484.2 → XP_024302252.1  F-actin-uncapping protein LRRC16A isoform X6

      UniProtKB/TrEMBL
      B2RTQ5
      Conserved Domains (5) summary
      sd00033
      Location:488 → 511
      LRR_RI; leucine-rich repeat [structural motif]
      sd00034
      Location:248 → 277
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam16000
      Location:790 → 1088
      CARMIL_C; CARMIL C-terminus
      cl26161
      Location:229 → 373
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      cl28033
      Location:1099 → 1348
      Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

    6. XM_024446485.2 → XP_024302253.1  F-actin-uncapping protein LRRC16A isoform X14

      UniProtKB/TrEMBL
      B2RTQ5
      Conserved Domains (5) summary
      sd00033
      Location:488 → 511
      LRR_RI; leucine-rich repeat [structural motif]
      sd00034
      Location:248 → 277
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam16000
      Location:790 → 1088
      CARMIL_C; CARMIL C-terminus
      cl26161
      Location:229 → 373
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      cl28033
      Location:1099 → 1345
      Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

    7. XM_017011011.2 → XP_016866500.1  F-actin-uncapping protein LRRC16A isoform X4

      UniProtKB/TrEMBL
      B2RTQ5

    8. XM_017011016.2 → XP_016866505.1  F-actin-uncapping protein LRRC16A isoform X13

      UniProtKB/TrEMBL
      B2RTQ5

    9. XM_017011013.2 → XP_016866502.1  F-actin-uncapping protein LRRC16A isoform X9

      UniProtKB/TrEMBL
      B2RTQ5

    10. XM_047418997.1 → XP_047274953.1  F-actin-uncapping protein LRRC16A isoform X15

    11. XM_017011010.2 → XP_016866499.1  F-actin-uncapping protein LRRC16A isoform X3

      UniProtKB/TrEMBL
      B2RTQ5

    12. XM_005249218.2 → XP_005249275.1  F-actin-uncapping protein LRRC16A isoform X7

      UniProtKB/TrEMBL
      B2RTQ5
      Conserved Domains (4) summary
      cd00116
      Location:229 → 373
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:484 → 507
      LRR_RI; leucine-rich repeat [structural motif]
      sd00034
      Location:248 → 277
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam16000
      Location:786 → 1078
      CARMIL_C; CARMIL C-terminus

    13. XM_047418994.1 → XP_047274950.1  F-actin-uncapping protein LRRC16A isoform X8

    14. XM_047418995.1 → XP_047274951.1  F-actin-uncapping protein LRRC16A isoform X10

    15. XM_047418996.1 → XP_047274952.1  F-actin-uncapping protein LRRC16A isoform X11

    16. XM_047418998.1 → XP_047274954.1  F-actin-uncapping protein LRRC16A isoform X16

    17. XM_047418999.1 → XP_047274955.1  F-actin-uncapping protein LRRC16A isoform X17

    18. XM_017011017.2 → XP_016866506.1  F-actin-uncapping protein LRRC16A isoform X18

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      25145130..25486328
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355815.1 → XP_054211790.1  F-actin-uncapping protein LRRC16A isoform X1

    2. XM_054355816.1 → XP_054211791.1  F-actin-uncapping protein LRRC16A isoform X2

    3. XM_054355828.1 → XP_054211803.1  F-actin-uncapping protein LRRC16A isoform X12

    4. XM_054355819.1 → XP_054211794.1  F-actin-uncapping protein LRRC16A isoform X5

    5. XM_054355820.1 → XP_054211795.1  F-actin-uncapping protein LRRC16A isoform X6

    6. XM_054355830.1 → XP_054211805.1  F-actin-uncapping protein LRRC16A isoform X14

    7. XM_054355818.1 → XP_054211793.1  F-actin-uncapping protein LRRC16A isoform X4

    8. XM_054355829.1 → XP_054211804.1  F-actin-uncapping protein LRRC16A isoform X13

    9. XM_054355823.1 → XP_054211798.1  F-actin-uncapping protein LRRC16A isoform X9

    10. XM_054355831.1 → XP_054211806.1  F-actin-uncapping protein LRRC16A isoform X15

    11. XM_054355817.1 → XP_054211792.1  F-actin-uncapping protein LRRC16A isoform X3

    12. XM_054355821.1 → XP_054211796.1  F-actin-uncapping protein LRRC16A isoform X7

    13. XM_054355822.1 → XP_054211797.1  F-actin-uncapping protein LRRC16A isoform X8

    14. XM_054355824.1 → XP_054211799.1  F-actin-uncapping protein LRRC16A isoform X10

    15. XM_054355825.1 → XP_054211800.1  F-actin-uncapping protein LRRC16A isoform X19

    16. XM_054355826.1 → XP_054211801.1  F-actin-uncapping protein LRRC16A isoform X20

    17. XM_054355827.1 → XP_054211802.1  F-actin-uncapping protein LRRC16A isoform X11

    18. XM_054355832.1 → XP_054211807.1  F-actin-uncapping protein LRRC16A isoform X16

    19. XM_054355833.1 → XP_054211808.1  F-actin-uncapping protein LRRC16A isoform X17

    20. XM_054355834.1 → XP_054211809.1  F-actin-uncapping protein LRRC16A isoform X18

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VZK9.1 GenPept UniProtKB/Swiss-Prot:Q5VZK9

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