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    CD99 CD99 molecule (Xg blood group) [ Homo sapiens (human) ]

    Gene ID: 4267, updated on 12-Nov-2024

    Summary

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    Official Symbol
    CD99provided by HGNC
    Official Full Name
    CD99 molecule (Xg blood group)provided by HGNC
    Primary source
    HGNC:HGNC:7082
    See related
    Ensembl:ENSG00000002586 Ensembl:ENSG00000292348 MIM:313470; MIM:450000; AllianceGenome:HGNC:7082
    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
    MIC2; HBA71; MIC2X; MIC2Y; MSK5X
    Summary
    The protein encoded by this gene is a cell surface glycoprotein involved in leukocyte migration, T-cell adhesion, ganglioside GM1 and transmembrane protein transport, and T-cell death by a caspase-independent pathway. In addition, the encoded protein may have the ability to rearrange the actin cytoskeleton and may also act as an oncosuppressor in osteosarcoma. This gene is found in the pseudoautosomal region of chromosomes X and Y and escapes X-chromosome inactivation. There is a related pseudogene located immediately adjacent to this locus. [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in fat (RPKM 38.2), gall bladder (RPKM 35.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CD99 in Genome Data Viewer
    Location:
    X;Y
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (2691295..2741309)
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (2691295..2741309)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (2304268..2354297)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (2368252..2418268)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (2609336..2659350)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (2559336..2609350)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 102 Neighboring gene microRNA 6089 Neighboring gene CD99 molecule pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:2699593-2700274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2700956-2701636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2701637-2702317 Neighboring gene Xg glycoprotein (Xg blood group) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2711950-2712538 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2717356-2718298 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2718299-2719240 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2721222-2721887 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:2722445-2723644 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:2764748-2764850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2766248-2766874 Neighboring gene glycogenin 2

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 3112 Neighboring gene long intergenic non-protein coding RNA 102 Neighboring gene microRNA 6089 Neighboring gene CD99 molecule pseudogene 1 Neighboring gene XG Y-linked 2 (pseudogene) Neighboring gene RNA, U6 small nuclear 1334, pseudogene

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RNA sequencing comparing centenarian and middle-aged women lymphoblastoid cell lines identifies age-related dysregulated expression of genes encoding selenoproteins, heat shock proteins, CD99, and BID.
      Title: RNA sequencing comparing centenarian and middle-aged women lymphoblastoid cell lines identifies age-related dysregulated expression of genes encoding selenoproteins, heat shock proteins, CD99, and BID.
    2. Sex- and species-specific contribution of CD99 to T cell costimulation during multiple sclerosis.
      Title: Sex- and species-specific contribution of CD99 to T cell costimulation during multiple sclerosis.
    3. CD99 Modulates the Proteomic Landscape of Ewing Sarcoma Cells and Related Extracellular Vesicles.
      Title: CD99 Modulates the Proteomic Landscape of Ewing Sarcoma Cells and Related Extracellular Vesicles.
    4. CD_99 G1 neutrophils modulate osteogenic differentiation of mesenchymal stem cells in the pathological process of ankylosing spondylitis.
      Title: CD_99 G1 neutrophils modulate osteogenic differentiation of mesenchymal stem cells in the pathological process of ankylosing spondylitis.
    5. Cell Adhesion Molecule CD99 in Cancer Immunotherapy.
      Title: Cell Adhesion Molecule CD99 in Cancer Immunotherapy.
    6. Role of CD99 in regulating homeostasis and differentiation in normal human epidermal keratinocytes.
      Title: Role of CD99 in regulating homeostasis and differentiation in normal human epidermal keratinocytes.
    7. CD99 in malignant hematopoiesis.
      Title: CD99 in malignant hematopoiesis.
    8. Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99.
      Title: Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99.
    9. CD99 and polymeric immunoglobulin receptor peptides deregulation in critical COVID-19: A potential link to molecular pathophysiology?
      Title: CD99 and polymeric immunoglobulin receptor peptides deregulation in critical COVID-19: A potential link to molecular pathophysiology?
    10. Tumour cell CD99 regulates transendothelial migration via CDC42 and actin remodelling.
      Title: Tumour cell CD99 regulates transendothelial migration via CDC42 and actin remodelling.
    Submit: New GeneRIF Correction See all GeneRIFs (94)

    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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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of CD99 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell extravasation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homotypic cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of neutrophil extravasation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in focal adhesion HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    CD99 antigen
    Names
    E2 antigen
    MIC2 (monoclonal antibody 12E7)
    T-cell surface glycoprotein E2
    antigen identified by monoclonal 12E7, Y homolog
    antigen identified by monoclonal antibodies 12E7, F21 and O13
    cell surface antigen 12E7
    cell surface antigen HBA-71
    cell surface antigen O13
    surface antigen MIC2

    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.

    Genomic

    1. NG_009174.1 RefSeqGene

      Range
      5109..55123
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1023

    mRNA and Protein(s)

    1. NM_001122898.3 → NP_001116370.1  CD99 antigen isoform b precursor

      See identical proteins and their annotated locations for NP_001116370.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) is shorter compared to isoform a.
      Source sequence(s)
      BC010109, DT216927
      Consensus CDS
      CCDS48071.1
      UniProtKB/TrEMBL
      B2R932
      Related
      ENSP00000370582.3, ENSP00000518650.1, ENST00000381187.8, ENST00000711164.1
      Conserved Domains (1) summary
      pfam12301
      Location:26 → 163
      CD99L2; CD99 antigen like protein 2

    2. NM_001321367.2 → NP_001308296.1  CD99 antigen isoform c precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR compared to variant 1, and encodes an isoform (c, also known as CD99sh) with a distinct, shorter C-terminus compared to isoform a.
      Source sequence(s)
      AC006209, BX402830, CX869233
      Consensus CDS
      CCDS75947.1
      UniProtKB/TrEMBL
      A8MQT7
      Related
      ENSP00000494027.1, ENSP00000518647.1, ENST00000482405.7, ENST00000711159.1
      Conserved Domains (1) summary
      pfam12301
      Location:26 → 160
      CD99L2; CD99 antigen like protein 2

    3. NM_001321368.2 → NP_001308297.1  CD99 antigen isoform d precursor

      Status: REVIEWED

      Source sequence(s)
      AC006209, BC002584, BI757712, CX869233
      Consensus CDS
      CCDS83452.1
      UniProtKB/TrEMBL
      A0A096LP69, B2R932
      Related
      ENSP00000485427.1, ENSP00000518646.1, ENST00000624481.4, ENST00000711158.1
      Conserved Domains (1) summary
      pfam12301
      Location:26 → 178
      CD99L2; CD99 antigen like protein 2

    4. NM_001321369.2 → NP_001308298.1  CD99 antigen isoform e precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) encodes an isoform (e) of the same length but different sequence than the isoform (f) encoded by variant 7.
      Source sequence(s)
      BC002584, CN299062, CX869233
      UniProtKB/TrEMBL
      B2R932
      Conserved Domains (1) summary
      pfam12301
      Location:34 → 162
      CD99L2; CD99 antigen like protein 2

    5. NM_001321370.2 → NP_001308299.1  CD99 antigen isoform f precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) encodes an isoform (f) of the same length but different sequence than the isoform (e) encoded by variant 6.
      Source sequence(s)
      AC006209
      UniProtKB/TrEMBL
      B2R932

    6. NM_002414.5 → NP_002405.1  CD99 antigen isoform a precursor

      See identical proteins and their annotated locations for NP_002405.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as type I) encodes the longest isoform (a, also known as CD99wt).
      Source sequence(s)
      BC010109
      Consensus CDS
      CCDS14119.1
      UniProtKB/Swiss-Prot
      A6NIW1, O00518, P14209, Q6ICV7
      UniProtKB/TrEMBL
      B2R932
      Related
      ENSP00000370588.3, ENSP00000518648.1, ENST00000381192.10, ENST00000711160.1
      Conserved Domains (1) summary
      pfam12301
      Location:26 → 179
      CD99L2; CD99 antigen like protein 2

    RNA

    1. NR_135623.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as type II) contains an alternate exon and uses an alternate splice junction in the 3' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC010109, U82164

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      2691295..2741309
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      2691295..2741309
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      2304268..2354297
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      2368252..2418268
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001277710.1: Suppressed sequence

      Description
      NM_001277710.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P14209.1 GenPept UniProtKB/Swiss-Prot:P14209

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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