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

Gene ID: 9473, updated on 3-Apr-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, Apr 2022]
Expression
Broad expression in bone marrow (RPKM 58.1), spleen (RPKM 43.6) and 17 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27872544..27886675)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27713266..27728777)
105.20220307 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. Icb-1 expression inhibits growth and fulvestrant response of breast cancer cells and affects survival of breast cancer patients. Riedmeier M, et al. Arch Gynecol Obstet, 2021 Jul. PMID 33389102
  2. Icb-1 gene polymorphism rs1467465 is associated with susceptibility to ovarian cancer. Schüler S, et al. J Ovarian Res, 2014. PMID 24826199, Free PMC Article
  3. icb-1 Gene counteracts growth of ovarian cancer cell lines. Treeck O, et al. Cancer Lett, 2013 Jul 28. PMID 23474491
  4. Network analysis of icb-1 gene function in human breast cancer cells. Treeck O, et al. J Cell Biochem, 2012 Sep. PMID 22565810
  5. 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

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)

Genotypes

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_2023_10

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

    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

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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