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CD163L1 Gene

protein-coding   GIFtS: 50
GCID: GC12M007507

CD163 Molecule-Like 1

(Previous name: CD163 antigen-like 1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
CD163 Molecule-Like 11 2     CD163 Antigen B2
CD163 Antigen-Like 11 2 3     Scavenger Receptor Cysteine-Rich Type 1 Protein M1602
CD163B2 3 5     CD163b Antigen3
M1602 3 5     CD164L15

External Ids:    HGNC: 303751   Entrez Gene: 2833162   Ensembl: ENSG000001776757   OMIM: 6060795   UniProtKB: Q9NR163   

Export aliases for CD163L1 gene to outside databases

Previous GC identifer: GC12M007399


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for CD163L1 Gene:
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. Alternatively
spliced transcript variants encoding different isoforms have been described but their full-length nature has not
been determined. (provided by RefSeq, Jul 2008)

GeneCards Summary for CD163L1 Gene:
CD163L1 (CD163 molecule-like 1) is a protein-coding gene. Diseases associated with CD163L1 include hepatitis b, and tonsillitis. GO annotations related to this gene include scavenger receptor activity. An important paralog of this gene is LOXL2.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000012.12  NT_009714.18  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CD163L1 gene promoter:
         MZF-1   FOXO1a   Evi-1   GATA-1   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCD163L1 promoter sequence
   Search Chromatin IP Primers for CD163L1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CD163L1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12p13.3   Ensembl cytogenetic band:  12p13.31   HGNC cytogenetic band: 12p13.31

CD163L1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CD163L1 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M007507:  view genomic region     (about GC identifiers)

Start:
7,499,281 bp from pter      End:
7,632,493 bp from pter
Size:
133,213 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: C163B_HUMAN, Q9NR16 (See protein sequence)
Recommended Name: Scavenger receptor cysteine-rich type 1 protein M160 precursor  
Size: 1453 amino acids; 159239 Da
Secondary accessions: B4E0G7 C9JHR7 E7EVK4 Q2M3B7 Q6UWC2
Alternative splicing: 4 isoforms:  Q9NR16-1   Q9NR16-2   Q9NR16-3   Q9NR16-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CD163L1: NX_Q9NR16

Explore proteomics data for CD163L1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn42, Asn78, Asn120, Asn161, Asn334, Asn377, Asn441, Asn548, Asn637, Asn972,
                                 Asn1013, Asn1084, Asn1104, Asn1161, Asn1171, Asn1318, Asn1354
  • Modification sites at PhosphoSitePlus

  • See CD163L1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_777601.2  
    ENSEMBL proteins: 
     ENSP00000438217   ENSP00000315945   ENSP00000393474   ENSP00000443004   ENSP00000439921  
     ENSP00000442328   ENSP00000379871  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR001190 SRCR
     IPR017448 Srcr_rcpt-rel

    Graphical View of Domain Structure for InterPro Entry Q9NR16

    ProtoNet protein and cluster: Q9NR16

    UniProtKB/Swiss-Prot: C163B_HUMAN, Q9NR16
    Similarity: Contains 12 SRCR domains


    CD163L1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005044scavenger receptor activity IEA--
         
    CD163L1 for ontologies           About GeneDecksing


    Animal Models:
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    hsa-mir-590-5p (MIRT040498)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    C163B_HUMAN, Q9NR16: Isoform 1: Cell membrane; Single-pass type I membrane protein (Probable)
    C163B_HUMAN, Q9NR16: Isoform 2: Cell membrane; Single-pass type I membrane protein (Probable)
    C163B_HUMAN, Q9NR16: Isoform 3: Secreted (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular4
    cytosol1
    endoplasmic reticulum1
    lysosome1
    nucleus1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    CD163L1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CD163L1
    Interactions:

        Search GeneGlobe Interaction Network for CD163L1

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CD163L1 (C163B)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for CD163L1 gene: 
    NM_174941.4  

    Unigene Cluster for CD163L1:

    CD163 molecule-like 1
    Hs.631727  [show with all ESTs]
    Unigene Representative Sequence: AK303372
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000539726 ENST00000542055 ENST00000543841 ENST00000313599(uc001qsy.3)
    ENST00000416109(uc010sge.2) ENST00000546182 ENST00000545597 ENST00000544331
    ENST00000545926 ENST00000543276 ENST00000396630
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      QuantiFast Probe-based Assays in human, mouse, rat CD163L1

    Additional mRNA sequence: 

    AF264014.1 AK058038.1 AK303372.1 BC104962.1 BC104964.1 GQ397482.1 

    3 DOTS entries:

    DT.208793  DT.100756478  DT.100705440 

    Selected AceView cDNA sequences (see all 38):

    BF792807 BQ024006 BQ776070 NM_174941 AA582301 W42792 AL529439 AK058038 
    BQ882211 AI609329 BF132072 BV177491 BX355217 BG570972 AF264014 AI278132 
    BV167606 AI738432 AI288981 AI095706 W42886 CA428959 AI090561 BX092497 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for CD163L1    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
    SP1:                                -                                                                                                   
    SP2:                                            -                                                                                       


    ECgene alternative splicing isoforms for CD163L1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CD163L1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTTGTGAAGA
    CD163L1 Expression
    About this image


    CD163L1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    CD163L1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CD163L1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631727

    UniProtKB/Swiss-Prot: C163B_HUMAN, Q9NR16
    Tissue specificity: Isoform 1 is highly expressed in the spleen, lymph nodes, thymus, and fetal liver and weakly
    expressed in bone marrow and no expression was found in peripheral blood leukocytes. Isoform 1 expression is
    restricted to the monocyte and macrophage cell lines. Isoform 2 is only expressed in spleen

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for CD163L1 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    --
    (see all 5)
    Uncharacterized protein
    (see all 5)
    39(a)
    39(a)
    (see all 5)
    many ↔ many
    many ↔ many
    (see all 5)
    JH376378.1(12420-16398)
    AADN03013081.1(2463-5190)
    zebrafish
    (Danio rerio)
    Actinopterygii si:dkey-21h14.126
    si:dkey-21h14.12
    21(a)
    many ↔ many
    4(10148733-10163063) ENSDARG00000094603
            Species with no ortholog for CD163L1

    ENSEMBL Gene Tree for CD163L1 (if available)
    TreeFam Gene Tree for CD163L1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CD163L1 gene
    LOXL22  CD62  LOXL42  CD1632  LOXL32  SSC5D2  PRSS122  CD5L2  
    LOX2  SRCRB4D2  LOXL12  DMBT12  
    7 SIMAP similar genes for CD163L1 using alignment to 6 protein entries:     C163B_HUMAN (see all proteins):
    CD163    SSC5D    LOXL2    LGALS3BP    CD5L    CD6
    DMBT1

    CD163L1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CD163L1 (see all 1861)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs770439481,2
    C,F--7391748(+) AATTAC/TACTAA 1 -- ds50011Minor allele frequency- T:0.03EA 120
    rs1416549911,2
    C--7391764(+) ACTACA/GAGAAC 1 -- ds50010--------
    rs1155179441,2
    --7391959(+) AGATCA/GGGGTG 1 -- ds50010--------
    rs1911062121,2
    C--7392101(+) CATGAA/GGGCTT 1 -- ds50010--------
    rs1827645421,2
    --7392121(+) GACATA/GATTAC 1 -- ds50010--------
    rs64881771,2
    C,F,H--7392136(+) CCAAAG/ACTCCA 1 -- ds500116Minor allele frequency- A:0.01NS NA WA CSA EA 918
    rs1505767231,2
    C--7392330(+) TTTTCC/TATAGG 1 -- ut310--------
    rs11297281,2
    C,F,A,H--7392332(-) GCCCTA/GTGGAA 1 -- ut31 ese318Minor allele frequency- G:0.23NS EA NA CSA WA 2341
    rs88151,2
    C,F,H--7392401(+) GTTGAT/GCTGAA 1 -- ut3122Minor allele frequency- G:0.13NS EA NA 2540
    rs1399767871,2
    --7392509(+) ACACAA/CACACA 1 -- int10--------

    HapMap Linkage Disequilibrium report for CD163L1 (7499281 - 7632493 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for CD163L1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2745488CNV Deletion23290073
    esv1408895CNV Insertion17803354
    nsv595CNV Insertion18451855
    nsv594CNV Loss18451855

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606079    OMIM disorders: --

    5 diseases for CD163L1:    
    About MalaCards
    hepatitis b    tonsillitis    hepatitis    thyroiditis
    cerebritis


    CD163L1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): CD163L1
    Human Genome Epidemiology (HuGE) Navigator: CD163L1 (2 documents)

    Export disorders for CD163L1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CD163L1 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with CD163L1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning of a novel scavenger receptor cysteine-rich type I transmembrane molecule (M160) expressed by human macrophages. (PubMed id 11086079)1, 2, 3 Groenlund J.... Holmskov U. (J. Immunol. 2000)
    2. 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. (PubMed id 11124526)1, 3, 9 Stover C.M....Holmskov U. (Cytogenet. Cell Genet. 2000)
    3. Identification of the CD163 protein domains involved in infection of the porcine reproductive and respiratory syndrome virus. (PubMed id 20032174)1, 2 Van Gorp H....Nauwynck H.J. (J. Virol. 2010)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    5. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PubMed id 15340161)1, 2 Zhang Z. and Henzel W.J. (Protein Sci. 2004)
    6. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    7. New genetic associations detected in a host response study to hepatitis B vaccine. (PubMed id 20237496)1 Davila S....Seielstad M. (Genes Immun. 2010)
    8. Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry. (PubMed id 19159218)2 Chen R.... Zou H. (J. Proteome Res. 2009)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    10. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (Nature 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 283316 HGNC: 30375 AceView: M160 Ensembl:ENSG00000177675 euGenes: HUgn283316
    ECgene: CD163L1 H-InvDB: CD163L1

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for CD163L1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CD163L1 gene:
    Search GeneIP for patents involving CD163L1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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