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

Gene ID: 9473, updated on 23-Nov-2023

Summary

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

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

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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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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_001039477.3NP_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:1862
    CABIT; Cell-cycle sustaining, positive selection,
  2. NM_001105556.3NP_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:265511
    CABIT; Cell-cycle sustaining, positive selection,
  3. NM_001286113.2NP_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:18235
    CABIT; Cell-cycle sustaining, positive selection,
  4. NM_001286115.2NP_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:18315
    CABIT; Cell-cycle sustaining, positive selection,
  5. NM_004848.4NP_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:18239
    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_006711050.2XP_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:18235
    CABIT; Cell-cycle sustaining, positive selection,
  2. XM_005246041.4XP_005246098.1  protein THEMIS2 isoform X2

    Conserved Domains (1) summary
    pfam12736
    Location:128374
    CABIT; Cell-cycle sustaining, positive selection,
  3. XM_011542445.3XP_011540747.1  protein THEMIS2 isoform X1

    See identical proteins and their annotated locations for XP_011540747.1

    Conserved Domains (1) summary
    pfam12736
    Location:218470
    CABIT; Cell-cycle sustaining, positive selection,
  4. XM_047434895.1XP_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_054339706.1XP_054195681.1  protein THEMIS2 isoform X3

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

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

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

    UniProtKB/TrEMBL
    H7C124