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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
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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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Related articles in PubMed

  1. Death induction by CD99 ligation in TEL/AML1-positive acute lymphoblastic leukemia and normal B cell precursors. Husak Z, et al. J Leukoc Biol, 2010 Aug. PMID 20453109
  2. CD99 type II is a determining factor for the differentiation of primitive neuroectodermal cells. Lee EJ, et al. Exp Mol Med, 2003 Oct 31. PMID 14646598
  3. Molecular mechanisms of CD99-induced caspase-independent cell death and cell-cell adhesion in Ewing's sarcoma cells: actin and zyxin as key intracellular mediators. Cerisano V, et al. Oncogene, 2004 Jul 22. PMID 15184883
  4. Solution structure of the cytoplasmic domain of human CD99 type I. Kim HY, et al. Mol Cells, 2004 Aug 31. PMID 15359120
  5. Prevalence of CD99 protein expression in pancreatic endocrine tumours (PETs). Goto A, et al. Histopathology, 2004 Oct. PMID 15469477

See all (157) citations in PubMed

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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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)

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

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