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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
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Genomic context

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See CLEC4F in Genome Data Viewer
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

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