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    THEMIS2 thymocyte selection associated family member 2 [ Homo sapiens (human) ]

    Gene ID: 9473, updated on 9-Dec-2024

    Summary

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    Official Symbol
    THEMIS2provided by HGNC
    Official Full Name
    thymocyte selection associated family member 2provided by HGNC
    Primary source
    HGNC:HGNC:16839
    See related
    Ensembl:ENSG00000130775 MIM:617856; AllianceGenome:HGNC:16839
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ICB1; ICB-1; C1orf38
    Summary
    Predicted to be involved in T cell receptor signaling pathway and regulation of B cell activation. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in bone marrow (RPKM 58.1), spleen (RPKM 43.6) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See THEMIS2 in Genome Data Viewer
    Location:
    1p35.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27872544..27886675)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27713266..27728777)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (28199055..28213186)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903885 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28156772-28157557 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28157558-28158342 Neighboring gene protein phosphatase 1 regulatory subunit 8 Neighboring gene small Cajal body-specific RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 574 Neighboring gene CRISPRi-validated cis-regulatory element chr1.3986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28206149-28206649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 577 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 578 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 532 Neighboring gene replication protein A2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28240839-28241343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28261145-28262046 Neighboring gene Sharpr-MPRA regulatory region 12823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28269804-28270304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28270305-28270805 Neighboring gene sphingomyelin phosphodiesterase acid like 3B

    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
    • 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. Silencing of the icb-1 gene inhibits the induction of differentiation-associated genes by vitamin D3 and all-trans retinoic acid in gynecological cancer cells. Haselberger M, et al. Int J Mol Med, 2011 Jul. PMID 21455565
    2. A novel basement membrane-induced gene identified in the human endometrial adenocarcinoma cell line HEC1B. Treeck O, et al. FEBS Lett, 1998 Apr 3. PMID 9563507
    3. Detection of increased icb-1 transcript levels in maturing HL-60 cells: a novel marker for granulocytic and monocytic in vitro differentiation. Treeck O, et al. Leuk Res, 2002 Aug. PMID 12191572
    4. Expression of icb-1 gene is interferon-gamma inducible in breast and ovarian cancer cell lines and affects the IFN gamma-response of SK-OV-3 ovarian cancer cells. Treeck O, et al. Cytokine, 2005 Nov 3. PMID 16219472
    5. Single nucleotide polymorphisms in human gene icb-1 and breast cancer susceptibility. Springwald A, et al. Cancer Invest, 2009 Jul. PMID 19308812

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Icb-1 expression inhibits growth and fulvestrant response of breast cancer cells and affects survival of breast cancer patients.
      Title: Icb-1 expression inhibits growth and fulvestrant response of breast cancer cells and affects survival of breast cancer patients.
    2. SNP rs1467465 of the human gene icb-1 might affect susceptibility to ovarian cancer.
      Title: Icb-1 gene polymorphism rs1467465 is associated with susceptibility to ovarian cancer.
    3. Loss of icb-1 expression accelerated proliferation of SK-OV-3, OVCAR-3 and OAW-42 cells and led to upregulation of ovarian cancer biomarkers like KLK10 and CLDN16.
      Title: icb-1 Gene counteracts growth of ovarian cancer cell lines.
    4. Data of this study suggest that icb-1 might exert a tumor-suppressor function in breast cancer and that its loss might confer relative resistance of breast cancer cells to apoptotic drugs.
      Title: Network analysis of icb-1 gene function in human breast cancer cells.
    5. Themis2 and Themis1 exhibit the same potential to restore T cell development and T cell receptor-mediated signaling in Themis1-deficient mice.
      Title: Interchangeability of Themis1 and Themis2 in thymocyte development reveals two related proteins with conserved molecular function.
    6. These findings together with the observed co-expression of icb-1 with E-cadherin in breast cancer samples support an important role of the icb-1 gene in cancer cell differentiation.
      Title: Silencing of the icb-1 gene inhibits the induction of differentiation-associated genes by vitamin D3 and all-trans retinoic acid in gynecological cancer cells.
    7. Data show that a highly significant positive correlation of icb-1 transcript levels with c-erbB2 (HER2) expression (p <.0001).
      Title: Icb-1 Gene expression is elevated in human endometrial adenocarcinoma and is closely associated with HER2 expression.
    8. 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.
    9. Identification of ICB-1 as a new player in endocrine-related cancer.
      Title: Knockdown of ICB-1 gene enhanced estrogen responsiveness of ovarian and breast cancer cells.
    10. Data suggest that SNP rs1467465 of human gene icb-1 might affect breast cancer susceptibility.
      Title: Single nucleotide polymorphisms in human gene icb-1 and breast cancer susceptibility.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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)

    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 receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell adhesion TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of B cell activation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein THEMIS2
    Names
    basement membrane-induced
    induced by contact to basement membrane 1 protein
    protein ICB-1
    thymocyte-expressed molecule involved in selection protein 2

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001039477.3 → NP_001034566.1  protein THEMIS2 isoform 2

      See identical proteins and their annotated locations for NP_001034566.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two coding exons, as compared to variant 3. The resulting isoform (2) has a much shorter and distinct C-terminus, compared to isoform 3.
      Source sequence(s)
      AL109927
      Consensus CDS
      CCDS30654.1
      UniProtKB/Swiss-Prot
      Q5TEJ8
      Related
      ENSP00000363037.3, ENST00000373927.7
      Conserved Domains (1) summary
      pfam12736
      Location:18 → 62
      CABIT; Cell-cycle sustaining, positive selection,

    2. NM_001105556.3 → NP_001099026.1  protein THEMIS2 isoform 3

      See identical proteins and their annotated locations for NP_001099026.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) encodes the longest isoform (3).
      Source sequence(s)
      AL109927, AL554503, BI908174
      Consensus CDS
      CCDS41290.1
      UniProtKB/Swiss-Prot
      A2RTZ3, B4DZT9, B4DZY3, O60560, Q5TEJ1, Q5TEJ8, Q5TEJ9, Q5TEK1, Q68DP4, Q9BYB6, Q9NS90
      Related
      ENSP00000363031.3, ENST00000373921.8
      Conserved Domains (1) summary
      pfam12736
      Location:265 → 511
      CABIT; Cell-cycle sustaining, positive selection,

    3. NM_001286113.2 → NP_001273042.1  protein THEMIS2 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an internal segment but maintains the reading frame compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AK303090, AL109927
      Consensus CDS
      CCDS65461.1
      UniProtKB/Swiss-Prot
      Q5TEJ8
      Related
      ENSP00000329862.7, ENST00000328928.11
      Conserved Domains (1) summary
      pfam12736
      Location:18 → 235
      CABIT; Cell-cycle sustaining, positive selection,

    4. NM_001286115.2 → NP_001273044.1  protein THEMIS2 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an altenate in-frame splice site compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
      Source sequence(s)
      AK303141, AL109927
      UniProtKB/Swiss-Prot
      Q5TEJ8
      Conserved Domains (1) summary
      pfam12736
      Location:18 → 315
      CABIT; Cell-cycle sustaining, positive selection,

    5. NM_004848.4 → NP_004839.2  protein THEMIS2 isoform 1

      See identical proteins and their annotated locations for NP_004839.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks an coding exon, as compared to variant 3. The resulting isoform (1) has a much shorter and distinct C-terminus, compared to isoform 3.
      Source sequence(s)
      AL109927, BC031655
      Consensus CDS
      CCDS30653.1
      UniProtKB/Swiss-Prot
      Q5TEJ8
      Related
      ENSP00000363035.1, ENST00000373925.5
      Conserved Domains (1) summary
      pfam12736
      Location:18 → 239
      CABIT; Cell-cycle sustaining, positive selection,

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      27872544..27886675
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006711050.2 → XP_006711113.1  protein THEMIS2 isoform X3

      See identical proteins and their annotated locations for XP_006711113.1

      UniProtKB/Swiss-Prot
      Q5TEJ8
      Conserved Domains (1) summary
      pfam12736
      Location:18 → 235
      CABIT; Cell-cycle sustaining, positive selection,

    2. XM_005246041.4 → XP_005246098.1  protein THEMIS2 isoform X2

      Conserved Domains (1) summary
      pfam12736
      Location:128 → 374
      CABIT; Cell-cycle sustaining, positive selection,

    3. XM_011542445.3 → XP_011540747.1  protein THEMIS2 isoform X1

      See identical proteins and their annotated locations for XP_011540747.1

      Conserved Domains (1) summary
      pfam12736
      Location:218 → 470
      CABIT; Cell-cycle sustaining, positive selection,

    4. XM_047434895.1 → XP_047290851.1  protein THEMIS2 isoform X4

      UniProtKB/TrEMBL
      H7C124
      Related
      ENSP00000398049.1, ENST00000456990.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      27713266..27728777
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339706.1 → XP_054195681.1  protein THEMIS2 isoform X3

    2. XM_054339705.1 → XP_054195680.1  protein THEMIS2 isoform X2

    3. XM_054339704.1 → XP_054195679.1  protein THEMIS2 isoform X1

    4. XM_054339707.1 → XP_054195682.1  protein THEMIS2 isoform X4

      UniProtKB/TrEMBL
      H7C124
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5TEJ8.1 GenPept UniProtKB/Swiss-Prot:Q5TEJ8

    Gene LinkOut

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

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