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    CLEC4F C-type lectin domain family 4 member F [ Homo sapiens (human) ]

    Gene ID: 165530, updated on 3-Apr-2024

    Summary

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    Official Symbol
    CLEC4Fprovided by HGNC
    Official Full Name
    C-type lectin domain family 4 member Fprovided by HGNC
    Primary source
    HGNC:HGNC:25357
    See related
    Ensembl:ENSG00000152672 MIM:620105; AllianceGenome:HGNC:25357
    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
    KCR; KCLR; CLECSF13
    Summary
    Predicted to enable galactose binding activity and glycolipid binding activity. Predicted to be involved in endocytosis. Predicted to act upstream of or within NK T cell activation. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in small intestine (RPKM 1.6), spleen (RPKM 1.4) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p13.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (70808643..70825235, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (70819694..70836320, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (71035775..71047731, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene folliculogenesis specific bHLH transcription factor Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:71027218-71027772 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 21 Neighboring gene MOB4 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:71057644-71058843 Neighboring gene CD207 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71091695-71092194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71114858-71115508 Neighboring gene long intergenic non-protein coding RNA 1143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71128841-71129734 Neighboring gene ventral anterior homeobox 2 Neighboring gene uncharacterized LOC124906188

    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. Structure of the gene for a carbohydrate-binding receptor unique to rat kupffer cells. Hoyle GW, et al. J Biol Chem, 1991 Jan 25. PMID 1846367
    2. Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. Navarini AA, et al. Nat Commun, 2014 Jun 13. PMID 24927181
    3. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Lim J, et al. Cell, 2006 May 19. PMID 16713569
    4. Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis. Tiemann K, et al. Oncogene, 2019 Apr. PMID 30575818, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ39110

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological process involved in interspecies interaction between organisms IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    C-type lectin domain family 4 member F
    Names
    C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13

    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_001258027.2 → NP_001244956.1  C-type lectin domain family 4 member F isoform 2

      See identical proteins and their annotated locations for NP_001244956.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and UTR compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC007395, AK301242, BC144652
      UniProtKB/TrEMBL
      B7Z704, B7ZMM1
      Conserved Domains (2) summary
      cd03590
      Location:471 → 547
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15619
      Location:264 → 429
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    2. NM_001321308.2 → NP_001308237.1  C-type lectin domain family 4 member F isoform 3

      Status: VALIDATED

      Source sequence(s)
      AK096429, BC139723, BU740367
      Consensus CDS
      CCDS82464.1
      UniProtKB/TrEMBL
      B7Z704
      Related
      ENSP00000390581.1, ENST00000426626.1
      Conserved Domains (2) summary
      cd03590
      Location:471 → 547
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      cl25732
      Location:120 → 448
      SMC_N; RecF/RecN/SMC N terminal domain

    3. NM_173535.3 → NP_775806.2  C-type lectin domain family 4 member F isoform 1

      See identical proteins and their annotated locations for NP_775806.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
      Source sequence(s)
      AC007395, AK096429, BU740367, CD701685
      Consensus CDS
      CCDS1910.1
      UniProtKB/Swiss-Prot
      A4QPA5, Q8N1N0
      UniProtKB/TrEMBL
      B7Z704
      Related
      ENSP00000272367.2, ENST00000272367.7
      Conserved Domains (2) summary
      cd03590
      Location:471 → 547
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15619
      Location:264 → 446
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      70808643..70825235 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017003519.1 → XP_016859008.1  C-type lectin domain family 4 member F isoform X1

      Conserved Domains (2) summary
      cd03590
      Location:581 → 657
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15921
      Location:207 → 581
      CCDC158; Coiled-coil domain-containing protein 158

    2. XM_011532637.2 → XP_011530939.1  C-type lectin domain family 4 member F isoform X1

      See identical proteins and their annotated locations for XP_011530939.1

      Conserved Domains (2) summary
      cd03590
      Location:581 → 657
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15921
      Location:207 → 581
      CCDC158; Coiled-coil domain-containing protein 158

    3. XM_011532642.3 → XP_011530944.1  C-type lectin domain family 4 member F isoform X6

      UniProtKB/TrEMBL
      B7Z704
      Conserved Domains (2) summary
      cd03590
      Location:441 → 517
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15619
      Location:234 → 416
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    4. XM_011532641.3 → XP_011530943.1  C-type lectin domain family 4 member F isoform X5

      Conserved Domains (1) summary
      pfam15619
      Location:374 → 556
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    5. XM_011532639.3 → XP_011530941.1  C-type lectin domain family 4 member F isoform X3

      UniProtKB/TrEMBL
      B7Z704
      Conserved Domains (2) summary
      cd03590
      Location:581 → 657
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15619
      Location:374 → 556
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    6. XM_011532638.3 → XP_011530940.1  C-type lectin domain family 4 member F isoform X2

      UniProtKB/TrEMBL
      B7Z704
      Conserved Domains (2) summary
      cd03590
      Location:581 → 657
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15619
      Location:374 → 556
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    7. XM_011532640.3 → XP_011530942.1  C-type lectin domain family 4 member F isoform X4

      UniProtKB/TrEMBL
      B7Z704
      Conserved Domains (2) summary
      cd03590
      Location:581 → 657
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15619
      Location:374 → 556
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    8. XM_011532635.3 → XP_011530937.1  C-type lectin domain family 4 member F isoform X1

      See identical proteins and their annotated locations for XP_011530937.1

      Conserved Domains (2) summary
      cd03590
      Location:581 → 657
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15921
      Location:207 → 581
      CCDC158; Coiled-coil domain-containing protein 158

    9. XM_011532643.1 → XP_011530945.1  C-type lectin domain family 4 member F isoform X7

      UniProtKB/TrEMBL
      B7Z704
      Conserved Domains (2) summary
      cd03590
      Location:410 → 486
      CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
      pfam15619
      Location:203 → 385
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      70819694..70836320 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340873.1 → XP_054196848.1  C-type lectin domain family 4 member F isoform X1

    2. XM_054340878.1 → XP_054196853.1  C-type lectin domain family 4 member F isoform X6

    3. XM_054340877.1 → XP_054196852.1  C-type lectin domain family 4 member F isoform X5

    4. XM_054340875.1 → XP_054196850.1  C-type lectin domain family 4 member F isoform X3

    5. XM_054340874.1 → XP_054196849.1  C-type lectin domain family 4 member F isoform X2

    6. XM_054340876.1 → XP_054196851.1  C-type lectin domain family 4 member F isoform X4

    7. XM_054340879.1 → XP_054196854.1  C-type lectin domain family 4 member F isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N1N0.2 GenPept UniProtKB/Swiss-Prot:Q8N1N0

    Gene LinkOut

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