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    CD109 CD109 molecule [ Homo sapiens (human) ]

    Gene ID: 135228, updated on 17-Jun-2024

    Summary

    Official Symbol
    CD109provided by HGNC
    Official Full Name
    CD109 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:21685
    See related
    Ensembl:ENSG00000156535 MIM:608859; AllianceGenome:HGNC:21685
    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
    p180; r150; CPAMD7
    Summary
    This gene encodes a glycosyl phosphatidylinositol (GPI)-linked glycoprotein that localizes to the surface of platelets, activated T-cells, and endothelial cells. The protein binds to and negatively regulates signalling by transforming growth factor beta (TGF-beta). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2014]
    Expression
    Broad expression in skin (RPKM 9.8), endometrium (RPKM 7.6) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CD109 in Genome Data Viewer
    Location:
    6q13
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (73679192..73828313)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (74857189..75006336)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (74405926..74538037)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17336 Neighboring gene EEF1A1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24752 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:74273247-74273796 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74275447-74275996 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74285738-74286453 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:74289636-74290835 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74291165-74292007 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94401 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94402 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94403 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94405 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74329139-74329367 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:74333473-74333650 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94408 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94412 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94411 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94413 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94414 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94416 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24754 Neighboring gene solute carrier family 17 member 5 Neighboring gene Sharpr-MPRA regulatory region 11313 Neighboring gene ribosomal protein S27 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74405769-74406483 Neighboring gene MPRA-validated peak5902 silencer Neighboring gene CD109 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 9272 Neighboring gene MPRA-validated peak5903 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74550244-74550817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:74560911-74561502 Neighboring gene uncharacterized LOC101928516 Neighboring gene thioredoxin pseudogene 7 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94479 Neighboring gene family with sequence similarity 136 member A pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Meta-analysis of genome-wide association studies identifies six new Loci for serum calcium concentrations.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD109 PubMed
    Vpu vpu Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD109 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ38569, FLJ41966, DKFZp762L1111

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables serine-type endopeptidase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transforming growth factor beta binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell surface HDA PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in platelet alpha granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    CD109 antigen
    Names
    150 kDa TGF-beta-1-binding protein
    C3 and PZP-like alpha-2-macroglobulin domain-containing protein 7
    Gov platelet alloantigens
    activated T-cell marker CD109
    platelet-specific Gov antigen

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_033971.1 RefSeqGene

      Range
      5419..137529
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1002

    mRNA and Protein(s)

    1. NM_001159587.3NP_001153059.1  CD109 antigen isoform 2 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AF410459, AK095888, AK130104, AL834478, AY788891, BM722643, BX107999, BX646244, CB529476, CB853216
      Consensus CDS
      CCDS55038.1
      UniProtKB/Swiss-Prot
      Q6YHK3
      Related
      ENSP00000388062.2, ENST00000437994.6
      Conserved Domains (6) summary
      COG2373
      Location:661000
      YfaS; Uncharacterized conserved protein YfaS, alpha-2-macroglobulin family [General function prediction only]
      cd02897
      Location:9071194
      A2M_2; Proteins similar to alpha2-macroglobulin (alpha (2)-M). This group also contains the pregnancy zone protein (PZP). Alpha(2)-M and PZP are broadly specific proteinase inhibitors. Alpha (2)-M is a major carrier protein in serum. The structural thioester ...
      pfam00207
      Location:693784
      A2M; Alpha-2-macroglobulin family
      pfam07677
      Location:12921379
      A2M_recep; A-macroglobulin receptor
      pfam07703
      Location:468599
      A2M_N_2; Alpha-2-macroglobulin family N-terminal region
      pfam17791
      Location:223301
      MG3; Macroglobulin domain MG3
    2. NM_001159588.3NP_001153060.1  CD109 antigen isoform 3 preproprotein

      See identical proteins and their annotated locations for NP_001153060.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AK130104, AL834478, BM722643, BX107999, BX641095, BX646244, CB529476, CB853216
      Consensus CDS
      CCDS55039.1
      UniProtKB/Swiss-Prot
      Q6YHK3
      Related
      ENSP00000404475.2, ENST00000422508.6
      Conserved Domains (6) summary
      cd02897
      Location:8301117
      A2M_2; Proteins similar to alpha2-macroglobulin (alpha (2)-M). This group also contains the pregnancy zone protein (PZP). Alpha(2)-M and PZP are broadly specific proteinase inhibitors. Alpha (2)-M is a major carrier protein in serum. The structural thioester ...
      pfam00207
      Location:616705
      A2M; Alpha-2-macroglobulin family
      pfam07677
      Location:12341318
      A2M_recep; A-macroglobulin receptor
      pfam07678
      Location:8821119
      A2M_comp; A-macroglobulin complement component
      pfam07703
      Location:393519
      A2M_N_2; Alpha-2-macroglobulin family N-terminal region
      cl19929
      Location:87144
      A2M_N; MG2 domain
    3. NM_133493.5NP_598000.2  CD109 antigen isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_598000.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AF410459, AK095888, AK130104, AL834478, BM722643, BX107999, BX646244, CB529476, CB853216
      Consensus CDS
      CCDS4982.1
      UniProtKB/Swiss-Prot
      A5YKK4, B2R948, B3KW25, Q0P6K7, Q5SYA8, Q5XUM7, Q5XUM9, Q6MZI7, Q6YHK3, Q8N3A7, Q8N915, Q8TDJ2, Q8TDJ3
      Related
      ENSP00000287097.4, ENST00000287097.6
      Conserved Domains (7) summary
      COG2373
      Location:661000
      YfaS; Uncharacterized conserved protein YfaS, alpha-2-macroglobulin family [General function prediction only]
      cd02897
      Location:9071194
      A2M_2; Proteins similar to alpha2-macroglobulin (alpha (2)-M). This group also contains the pregnancy zone protein (PZP). Alpha(2)-M and PZP are broadly specific proteinase inhibitors. Alpha (2)-M is a major carrier protein in serum. The structural thioester ...
      pfam00207
      Location:693782
      A2M; Alpha-2-macroglobulin family
      pfam01835
      Location:130221
      A2M_N; MG2 domain
      pfam07677
      Location:13111395
      A2M_recep; A-macroglobulin receptor
      pfam07678
      Location:9591196
      A2M_comp; A-macroglobulin complement component
      pfam07703
      Location:470596
      A2M_N_2; Alpha-2-macroglobulin family N-terminal region

    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
      73679192..73828313
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418211.1XP_047274167.1  CD109 antigen isoform X1

    2. XM_047418212.1XP_047274168.1  CD109 antigen isoform X2

    3. XM_047418215.1XP_047274171.1  CD109 antigen isoform X2

    4. XM_047418213.1XP_047274169.1  CD109 antigen isoform X2

    5. XM_047418216.1XP_047274172.1  CD109 antigen isoform X2

    6. XM_047418214.1XP_047274170.1  CD109 antigen isoform X2

    7. XM_047418217.1XP_047274173.1  CD109 antigen isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      74857189..75006336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354302.1XP_054210277.1  CD109 antigen isoform X1

    2. XM_054354304.1XP_054210279.1  CD109 antigen isoform X2

    3. XM_054354303.1XP_054210278.1  CD109 antigen isoform X2

    4. XM_054354305.1XP_054210280.1  CD109 antigen isoform X2

    5. XM_054354306.1XP_054210281.1  CD109 antigen isoform X2

    6. XM_054354307.1XP_054210282.1  CD109 antigen isoform X3