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LTB Gene

protein-coding   GIFtS: 60

GC06M031656
lymphotoxin beta (TNF superfamily, member 3)
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: TNFC)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
LT-beta 3
OTTHUMP00000029185 2
OTTHUMP00000038214 2
TNF-C 3
TNFC 2, 3, 5
TNFSF3 1, 2, 3
lymphotoxin-beta 2
p33 1, 2
Descriptions
Tumor necrosis factor C 2, 3
Tumor necrosis factor ligand superfamily member 3 3
lymphotoxin beta (TNF superfamily, member 3) 2
External Ids
HGNC: 67111
Entrez Gene: 40502
UniProtKB: Q066433
Ensembl: ENSG000002044877
Search outside databases for aliases for LTB gene

Previous GC identifers: GC06M031611 GC06M031602 GC06M031319 GC06M031652

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for LTB:
Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to
the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is
the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex
is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphotoxin-alpha
2/beta 1. LTB is an inducer of the inflammatory response system and involved in normal development
of lymphoid tissue. Lymphotoxin-beta isoform b is unable to complex with lymphotoxin-alpha
suggesting a function for lymphotoxin-beta which is independent of lympyhotoxin-alpha. Alternative
splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq]

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

Gene Wiki entry for LTB

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the LTB gene  

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.3

LTB Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M031656:     (about GC identifiers)

Start:
31,656,314 bp from pter
End:
31,658,181 bp from pter
Size:
1,868 bases
Orientation:
minus strand

2 alternative locations:
Chr6-,c6_QBL 31,681,431-31,683,298      Chr6-,c6_COX 31,683,001-31,684,868     
RefSeq DNA sequence:
NC_000006.10  NT_007592.14  NT_113891.1  NT_113894.1  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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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
Subcellular location: Membrane; Single-pass type II membrane protein (Potential)
Secondary accessions: P78370 Q99761
Alternative splicing: 2 isoforms:  Q06643-1   Q06643-2   

REFSEQ proteins (2 alternative transcripts): 
NP_002332.1  NP_033666.1  


ENSEMBL proteins: 
ENSP00000365283 ENSP00000365285 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Sigma-Aldrich Proteins for LTB  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Lymphotoxin Beta)
Browse Abnova for Human Recombinant Proteins
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

4 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005575 cellular_component ND9299492
GO:0005615 extracellular space IEA--
GO:0016020 membrane IEA--
GO:0016021 integral to membrane IEA--
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Antibodies for LTB: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Browse Antibodies at Sigma-Aldrich
R&D Systems Antibodies for LTB (Lymphotoxin beta/TNFSF3)
Antibodies from Abcam (Lymphotoxin Beta), each with their AbpromiseSM
Browse Abnova for Monoclonal and Polyclonal Antibodies
Search Novus for antibodies for LTB

Assays for LTB: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

4 InterPro domains/families:
 IPR002961 TNF_C
 IPR006052 TNF_family
 IPR006053 TNF_abc
 IPR008983 Tumour_necrosis_fac-like


   GeneDecks  LTB for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry Q06643

ProtoNet protein and cluster: Q06643

3 Blocks protein families:
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

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (LTB)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_009588

              Applied Biosystems Silencer® siRNAs for LTB

              Sigma-Aldrich siRNA and siRNA Panels for LTB  
                     Sigma-Aldrich shRNA Panels and shRNA for LTB  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for LTB
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_002341
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_002341
                                 untagged cDNA clones in CMV expression vector (see all 3): NM_002341 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_002341

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

Genatlas biochemistry entry for LTB:
lymphotoxin beta,expressed in macrophages,,tumors necrosis factor (ligand) superfamily,member 3

6 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Ltb):

hematopoietic systemimmune systemlife span-post-weaning/agingliver/biliary systemno phenotypic analysis
respiratory system

2 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005125 cytokine activity IEA--
GO:0005164 tumor necrosis factor receptor binding IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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1 Millipore Pathway for LTB
 Apoptosis and survival Lymphotoxin-beta receptor signaling

   GeneDecks  LTB for the pathways selected above  
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2 Sigma-Aldrich "Your Favorite Gene" Pathways for  LTB  (Your Favorite Gene powered by Ingenuity) 
 Lymphotoxin &beta
 Dendritic Cell Maturation

   GeneDecks  LTB for the pathways selected above  
About GeneDecksing

1 Kegg Pathway  (Kegg details for LTB):
 hsa04060 Cytokine-cytokine receptor interaction

   GeneDecks  LTB for the pathways selected above  
About GeneDecksing
 Gene Network CentralTM Interacting Genes and Proteins Network for  LTB 


5 Interacting proteins for LTB (ENSP000003652853) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
LTBRENSP000002289183STRING (score=.985)
NCR3ENSP000003421563STRING (score=.847)
TNFRSF1AENSP000001627493STRING (score=.845)
TNFRSF1BENSP000003654353STRING (score=.794)
IFNGENSP000002291353STRING (score=.773)
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5/20 Gene Ontology (GO) biological process terms (links to tree view) (see all 20 ):

GO IDQualified GO termEvidencePubMed IDs
GO:0001775 cell activation IEA--
GO:0002037 negative regulation of L-glutamate transport IEA--
GO:0006915 apoptosis IEA--
GO:0006917 induction of apoptosis IEA--
GO:0006955 immune response IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for LTB
1 Novoseek chemical compound relationship for LTB gene
Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
rantes 40.32 3 11818457 (1), 12828562 (1), 10544185 (1)
About this table


(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (LTB)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_009588

              Sigma-Aldrich siRNA and siRNA Panels for LTB  
                     Sigma-Aldrich shRNA Panels and shRNA for LTB  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_002341  NM_009588  

REFSEQ mRNAs for LTB gene (2 alternative transcripts): 

NM_002341.1   NM_009588.1   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_002341  NM_009588  

               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_002341
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_002341
                                 untagged cDNA clones in CMV expression vector (see all 3): NM_002341 

Additional cDNA sequence: 

AK095821.1 AK312210.1 BC055090.1 BC069330.1 BC093783.1 L11015.1 U79029.1 U89922.1 

7 DOTS entries:

DT.210387  DT.92422644  DT.99936177  DT.100743069  DT.95215874  DT.446271  DT.95281755 

13 AceView cDNA sequences:

BC069330 BX095063 NM_002341 NM_009588 U79029 L11015 U89922 AK095821 
BC055090 AW978651 BC018898 AA847198 AA836521 

highest scoring ESTs for LTB:

BC069330 L11015 U79029 U89922 AA836521 AA847198 AW978651 BC055090 BC093783 BF238152 

Unigene Cluster for LTB:

Lymphotoxin beta (TNF superfamily, member 3)
Hs.376208  [show with all ESTs]
Unigene Representative Sequence: AK095821


GeneLoc Exon Structure

2 Ensembl transcripts including schematic representations:
ENST00000376115  ENST00000376117  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

LTB expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for LTB

1 / 2 / 3

3 probe-sets matching LTB gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
40729_s_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 Y14768 0.20 0.50 0.38 1

207339_s_at2, 3 U133-A 1 1.00 1.00 -- -- NM_002341 0.60 1.00 0.82 1

207339_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  LTB for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: GCAGTGGGAA

SOURCE GeneReport for Unigene cluster: Hs.376208

Expression variation in blood from EXPOLDB for LTB

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

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for LTB gene from 5 species
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
LTB1   -- lymphotoxin beta (TNF superfamily, member 3) 84.56(n)
81.15(a)
481712  XM_538833.2  XP_538833.2 
chimpanzee
(Pan troglodytes)
LTB1   -- lymphotoxin beta (TNF superfamily, member 3) 99.73(n)
99.59(a)
744486  XM_001153356.1  XP_001153356.1 
cow
(Bos taurus)
LTB1   -- lymphotoxin beta (TNF superfamily, member 3) 84.29(n)
80.33(a)
529757  XM_608214.3  XP_608214.2 
rat
(Rattus norvegicus)
Ltb1   -- lymphotoxin beta (TNF superfamily, member 3) 80.69(n)
75.83(a)
361795  NM_212507.2  NP_997672.1 
mouse
(Mus musculus)
Ltb1, 5 17 (19.06 cM)5
lymphotoxin B1, 5 79.97(n)1
74.7(a)1
169941  NM_008518.11  NP_032544.11 
 AF1097195  AI6628015  (see all 12)
About this table        Species with no ortholog for LTB

ENSEMBL Gene Tree for LTB
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

  --
(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/49 NCBI SNPs in LTB are shown (see all 49 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 90)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 6 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs30935541,2
C,F,H31657386(-) TCCAGG/AGTTTC 2 E/G S/G mis1 ese313Minor allele frequency- A:0.01NS EU EA WA NA 1064
rs7691751,2
C,F,H31656347(-) TGAAAA/GTAAAG 2 -- ut317Minor allele frequency- G:0.00NA NS MN EU EA WA 870
rs30935621,2
C,F,H31659516(-) gtctgG/Cgtgac 2 -- ng3114Minor allele frequency- C:0.03NS EU EA WA NA 1236
--
rs7691741,2
A,C,F31659045(-) ccaaaG/Ctgttg 2 -- ng314Minor allele frequency- C:0.12NA NS 432
rs30935561,2
C,F,H31656430(-) GAATAT/CTGGGG 2 -- ut31 ese38Minor allele frequency- C:0.01NS EU EA WA 822
rs77669881,2
F,H31659326(+) GTCAAG/CGGAAG 2 -- ng31 trp34Minor allele frequency- C:0.01EU EA WA 410
rs20220451,2
C,H31658539(-) TTGAGG/AGTATA 2 -- ng316Minor allele frequency- A:0.00MN EU EA WA NA 659
--
rs42481651,2
C,F31656507(+) CTCGCG/AAAGTC 2 F/F syn1 ut312Minor allele frequency- A:0.01NS 324
--
rs30935501,2
C,F31658518(-) AACCAC/TATTGG 2 -- ng31 tfbs36Minor allele frequency- T:0.01NS NA 408
rs46458461,2
F,H31656245(+) GAAGAG/CTACTG 2 -- ng515Minor allele frequency- C:0.01NS EU EA WA 556
About this table

HapMap Linkage Disequilibrium images for LTB (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 600978

10 Novoseek disease relationships for LTB gene

Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
necrosis 60.11 15 9307242 (1), 12912866 (1), 15969671 (1), 10358762 (1) (see all 13)
synovitis 42.17 1 15248211 (1)
tumors 40.60 16 9299492 (2), 7995952 (1), 9307242 (1), 10358762 (1) (see all 13)
herpes 27.61 1 10358762 (1)
hepatitis c 18.53 1 12912866 (1)
inflammation 17.10 4 18379788 (1), 18292573 (1), 11747624 (1)
hepatitis c chronic 16.08 2 12912866 (1)
lymphoma non-hodgkins 4.98 1 9299492 (1)
leukemia 1.99 2 12801841 (1)
liver diseases 0.00 2 12912866 (1)
About this table

Genetic Association Database: LTB
Human Genome Epidemiology Navigator: LTB (6 documents)

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

10/87 PubMed articles for LTB gene (see all 87 ):
(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 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, and/or H-InvDB)
About This Section

Entrez Gene: 4050 HGNC: 6711 AceView: LTB Ensembl:ENSG00000204487 euGenes: HUgn4050
ECgene: LTB H-InvDB: LTB
(According to HUGE)
About This Section

  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

NameDescription
ATLAS Chromosomes in Cancer entry for LTB Genetics and Cytogenetics in Oncology and Haematology
NIEHS-SNPshttp://egp.gs.washington.edu/data/ltb/
SeattleSNPshttp://pga.gs.washington.edu/data/ltb/
(Available from WIS Yeda, Salk, Tufts)
About This Section

  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for LTB:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
  Invitrogen Clones  Invitrogen Q-PCR Products
  Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for LTB-related products

 Millipore Custom Antibody & Bulk Services
 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for LTB Browse antibodies at Sigma-Aldrich
 Explore super-pooled esiRNAs Proteins for LTB
 Lentivirus-delivered shRNAs for LTB Browse small molecules at Sigma-Aldrich
 "Your Favorite Gene" Pathwaysfeedback


  
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 Recombinant Proteins
(Lymphotoxin Beta)
 Antibodies (Lymphotoxin Beta)
 Search OriGene for LTB
 Search Tocris compounds for LTB




 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Search Novus for antibodies for LTB

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