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    CD163L1 CD163 molecule like 1 [ Homo sapiens (human) ]

    Gene ID: 283316, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CD163L1provided by HGNC
    Official Full Name
    CD163 molecule like 1provided by HGNC
    Primary source
    HGNC:HGNC:30375
    See related
    Ensembl:ENSG00000177675 MIM:606079; AllianceGenome:HGNC:30375
    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
    WC1; M160; STAR; CD163B; SCARI2
    Summary
    This gene encodes a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Members of this family are secreted or membrane-anchored proteins mainly found in cells associated with the immune system. The SRCR family is defined by a 100-110 amino acid SRCR domain, which may mediate protein-protein interaction and ligand binding. The encoded protein contains twelve SRCR domains, a transmembrane region and a cytoplasmic domain. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]
    Expression
    Broad expression in spleen (RPKM 7.7), small intestine (RPKM 4.5) and 14 other tissues See more
    Orthologs
    all
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    Genomic context

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    See CD163L1 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7318768..7444153, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7332108..7457540, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7507556..7596749, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7341269-7341768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7340767-7341268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342139-7342855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342856-7343571 Neighboring gene peroxisomal biogenesis factor 5 Neighboring gene acyl-CoA synthetase medium chain family member 6 pseudogene Neighboring gene MPRA-validated peak1554 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr12:7434099-7434654 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:7469109-7470308 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:7476238-7477437 Neighboring gene uncharacterized LOC101927882 Neighboring gene acyl-CoA synthetase medium chain family member 4 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:7521391-7522590 Neighboring gene M-phase phosphoprotein 8 pseudogene Neighboring gene uncharacterized LOC124902870 Neighboring gene NANOG hESC enhancer GRCh37_chr12:7650144-7650645 Neighboring gene CD163 molecule Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_30893 Neighboring gene MPRA-validated peak1556 silencer Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 31

    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. Antagonistic regulation of macrophage phenotype by M-CSF and GM-CSF: implication in atherosclerosis. Brochériou I, et al. Atherosclerosis, 2011 Feb. PMID 21159337
    2. Identification of the CD163 protein domains involved in infection of the porcine reproductive and respiratory syndrome virus. Van Gorp H, et al. J Virol, 2010 Mar. PMID 20032174, Free PMC Article
    3. Cloning of a novel scavenger receptor cysteine-rich type I transmembrane molecule (M160) expressed by human macrophages. Gronlund J, et al. J Immunol, 2000 Dec 1. PMID 11086079
    4. CD163L1(+)CXCL10(+) Macrophages are Enriched Within Colonic Lamina Propria of Diverticulitis Patients. Schieffer KM, et al. J Surg Res, 2021 Nov. PMID 34256195
    5. Assignment of CD163B, the gene encoding M160, a novel scavenger receptor, to human chromosome 12p13.3 by in situ hybridization and somatic cell hybrid analysis. Stover CM, et al. Cytogenet Cell Genet, 2000. PMID 11124526

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CD163L1(+)CXCL10(+) Macrophages are Enriched Within Colonic Lamina Propria of Diverticulitis Patients.
      Title: CD163L1(+)CXCL10(+) Macrophages are Enriched Within Colonic Lamina Propria of Diverticulitis Patients.
    2. 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.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    Submit: New GeneRIF Correction

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env A synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of CD163 molecule-like 1 (CD163L1) in peptide-treated PBMCs PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    scavenger receptor cysteine-rich type 1 protein M160
    Names
    CD163 antigen B
    CD163 antigen-like 1

    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_001297650.2 → NP_001284579.2  scavenger receptor cysteine-rich type 1 protein M160 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC131205, AC131206, AC131207
      Consensus CDS
      CCDS73434.1
      Related
      ENSP00000393474.2, ENST00000416109.2
      Conserved Domains (2) summary
      smart00202
      Location:1046 → 1146
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:1161 → 1253
      SRCR; Scavenger receptor cysteine-rich domain

    2. NM_174941.6 → NP_777601.3  scavenger receptor cysteine-rich type 1 protein M160 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC131205, AC131206, AC131207
      Consensus CDS
      CCDS8577.1
      UniProtKB/Swiss-Prot
      B4E0G7, C9JHR7, E7EVK4, Q2M3B7, Q6UWC2, Q9NR16
      Related
      ENSP00000315945.3, ENST00000313599.8
      Conserved Domains (2) summary
      smart00202
      Location:1036 → 1136
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:1151 → 1243
      SRCR; Scavenger receptor cysteine-rich domain

    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
      7318768..7444153 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520616.2 → XP_011518918.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X1

      UniProtKB/Swiss-Prot
      Q9NR16
      Conserved Domains (2) summary
      smart00202
      Location:1036 → 1136
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:1041 → 1136
      SRCR; Scavenger receptor cysteine-rich domain

    2. XM_011520617.3 → XP_011518919.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X2

      Conserved Domains (2) summary
      smart00202
      Location:1011 → 1111
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:1016 → 1111
      SRCR; Scavenger receptor cysteine-rich domain

    3. XM_011520620.2 → XP_011518922.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X4

      See identical proteins and their annotated locations for XP_011518922.1

      Conserved Domains (2) summary
      smart00202
      Location:765 → 865
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:770 → 865
      SRCR; Scavenger receptor cysteine-rich domain

    4. XM_011520619.2 → XP_011518921.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X4

      See identical proteins and their annotated locations for XP_011518921.1

      Conserved Domains (2) summary
      smart00202
      Location:765 → 865
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:770 → 865
      SRCR; Scavenger receptor cysteine-rich domain

    5. XM_011520618.4 → XP_011518920.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X3

      Conserved Domains (2) summary
      smart00202
      Location:797 → 897
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:802 → 897
      SRCR; Scavenger receptor cysteine-rich domain

    6. XM_011520621.4 → XP_011518923.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X5

      Conserved Domains (2) summary
      smart00202
      Location:349 → 449
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:354 → 449
      SRCR; Scavenger receptor cysteine-rich domain

    RNA

    1. XR_931282.3 RNA Sequence

    2. XR_007063068.1 RNA Sequence

    3. XR_007063067.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      7332108..7457540 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371768.1 → XP_054227743.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X1

    2. XM_054371769.1 → XP_054227744.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X2

    3. XM_054371772.1 → XP_054227747.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X4

    4. XM_054371771.1 → XP_054227746.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X4

    5. XM_054371770.1 → XP_054227745.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X3

    6. XM_054371773.1 → XP_054227748.1  scavenger receptor cysteine-rich type 1 protein M160 isoform X5

    RNA

    1. XR_008488566.1 RNA Sequence

    2. XR_008488565.1 RNA Sequence

    3. XR_008488564.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NR16.2 GenPept UniProtKB/Swiss-Prot:Q9NR16

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