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ENSG00000223448 Gene

protein-coding   GIFtS: 13
GCID: GC06Ml31587          (predicted)

ENSG00000223448


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at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
LT-beta3
TNF-C3
TNFC3
TNFSF33
Tumor Necrosis Factor C3
Tumor Necrosis Factor Ligand Superfamily Member 33

External Ids:    Ensembl: ENSG000002234487   UniProtKB: Q066433   

Export aliases for ENSG00000223448 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ENSG00000223448 Gene:
ENSG00000223448 is a protein-coding gene.

UniProtKB/Swiss-Prot: TNFC_HUMAN, Q06643
Function: Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides
the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably
non-functional




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for ENSG00000223448
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ENSG00000223448


Genomic Location:
Chromosome:6   

Ensembl cytogenetic band:  HSCHR6_MHC_MANNp22.1   

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06Ml31587:       (about GC identifiers)

Start:
31,587,819 bp from start of contig ALT_REF_LOCI_4      End:
31,589,786 bp from start of contig ALT_REF_LOCI_4
Size:
1,968 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
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UniProtKB/Swiss-Prot: TNFC_HUMAN, Q06643 (See protein sequence)
Recommended Name: Lymphotoxin-beta  
Size: 244 amino acids; 25390 Da
Subunit: Heterotrimer of either two LTB and one LTA subunits or (less prevalent) one LTB and two LTA subunits
1 PDB 3D structure from and Proteopedia for ENSG00000223448:
4MXW (3D)    
Secondary accessions: P78370 Q52LU8 Q99761
Alternative splicing: 2 isoforms:  Q06643-1   Q06643-2   

Explore the universe of human proteins at neXtProt for ENSG00000223448: NX_Q06643

Explore proteomics data for ENSG00000223448 at MOPED


See ENSG00000223448 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000398741  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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5 InterPro protein domains:
 IPR002961 TNF_C
 IPR006052 TNF_dom
 IPR006053 TNF
 IPR008983 Tumour_necrosis_fac-like_dom
 IPR021184 TNF_CS

Graphical View of Domain Structure for InterPro Entry Q06643

ProtoNet protein and cluster: Q06643

3 Blocks protein domains:
IPB002961 Tumour necrosis factor c (lymphotoxin-beta) signature
IPB006052 Tumor Necrosis Factor
IPB006053 Tumour necrosis factor family signature


UniProtKB/Swiss-Prot: TNFC_HUMAN, Q06643
Similarity: Belongs to the tumor necrosis factor family


Find genes that share domains with ENSG00000223448           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: TNFC_HUMAN, Q06643
Function: Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides
the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably
non-functional

     Gene Ontology (GO): 4 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005102receptor binding ----
GO:0005125cytokine activity ----
GO:0005164tumor necrosis factor receptor binding ----
GO:0005515protein binding ----
     
Find genes that share ontologies with ENSG00000223448           About GenesLikeMe


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
TNFC_HUMAN, Q06643: Membrane; Single-pass type II membrane protein (Potential)

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ----
GO:0005615extracellular space ----
GO:0016020membrane ----
GO:0016021integral component of membrane ----

Find genes that share ontologies with ENSG00000223448           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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Interactions:

    Search GeneGlobe Interaction Network for ENSG00000223448

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

Selected Interacting proteins for ENSG00000223448 (Q066433 ENSP000003987414) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
InteractantInteraction Details
GeneCardExternal ID(s)
ENSG00000230279P013743I2D: score=4 
ENSG00000231408P013743I2D: score=4 
LTAP013743I2D: score=4 
LTBRP369413I2D: score=3 
TNFRSF1AP194383I2D: score=3 
About this table

Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006955immune response ----
GO:0007165signal transduction ----
GO:0007267cell-cell signaling ----
GO:0010467gene expression ----
GO:0043588skin development ----

Find genes that share ontologies with ENSG00000223448           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for ENSG00000223448 (TNFC)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000420402(uc011gym.1) ENST00000468184(uc011gyn.1) ENST00000496765

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GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

ENSG00000223448 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

ENSG00000223448 Protein Expression

UniProtKB/Swiss-Prot: TNFC_HUMAN, Q06643
Tissue specificity: Spleen and thymus

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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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  --

ENSEMBL Gene Tree for ENSG00000223448 (if available)
TreeFam Gene Tree for ENSG00000223448 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for ENSG00000223448 gene integrated from 10 sources:
(articles sorted by number of sources associating them with ENSG00000223448)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. (PubMed id 14656967)2 Xie T.... Hood L. (Genome Res. 2003)
  4. A new member of the Ig superfamily and a V-ATPase G subunit are among the predicted products of novel genes close to the TNF locus in the human MHC. (PubMed id 10202016)2 Neville M.J. and Campbell R.D. (J. Immunol. 1999)
  5. Identification of two lymphotoxin beta isoforms expressed in human lymphoid cell lines and non-Hodgkin's lymphomas. (PubMed id 9299492)2 Warzocha K....Salles G. (Biochem. Biophys. Res. Commun. 1997)
  6. Lymphotoxin beta, a novel member of the TNF family that forms a heteromeric complex with lymphotoxin on the cell surface. (PubMed id 7916655)2 Browning J.L.... Ware C.F. (Cell 1993)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Ensembl:ENSG00000223448

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
NIEHS-SNPshttp://egp.gs.washington.edu/data/ltb/
SeattleSNPshttp://pga.gs.washington.edu/data/ltb/

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for ENSG00000223448 gene:
Search GeneIP for patents involving ENSG00000223448

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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