Summary: Linker for activation of T-cells family member 2
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This is the Wikipedia entry entitled "LAT2". More...
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|, LAB, NTAL, WBSCR15, WBSCR5, WSCR5, HSPC046, linker for activation of T-cells family member 2, linker for activation of T cells family member 2|
This gene is one of the contiguous genes at 7q11.23 commonly deleted in Williams syndrome, a multisystem developmental disorder. This gene consists of at least 14 exons, and its alternative splicing generates 3 transcript variants, all encoding the same protein.
- GRCh38: Ensembl release 89: ENSG00000086730 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000040751 - Ensembl, May 2017
- "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- Osborne LR, Martindale D, Scherer SW, Shi XM, Huizenga J, Heng HH, Costa T, Pober B, Lew L, Brinkman J, Rommens J, Koop B, Tsui LC (Jan 1997). "Identification of genes from a 500-kb region at 7q11.23 that is commonly deleted in Williams syndrome patients". Genomics. 36 (2): 328â€“36. doi:10.1006/geno.1996.0469. PMID 8812460.
- Janssen E, Zhu M, Zhang W, Koonpaew S, Zhang W (Jan 2003). "LAB: a new membrane-associated adaptor molecule in B cell activation". Nat Immunol. 4 (2): 117â€“23. doi:10.1038/ni882. PMID 12514734.
- "Entrez Gene: LAT2 linker for activation of T cells family, member 2".
- Rivera J (2005). "NTAL/LAB and LAT: a balancing act in mast-cell activation and function". Trends Immunol. 26 (3): 119â€“22. doi:10.1016/j.it.2005.01.001. PMID 15745852.
- Maruyama K, Sugano S (1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1â€“2): 171â€“4. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
- PÃ©rez Jurado LA, Peoples R, Kaplan P, et al. (1996). "Molecular definition of the chromosome 7 deletion in Williams syndrome and parent-of-origin effects on growth". Am. J. Hum. Genet. 59 (4): 781â€“92. PMC 1914804. PMID 8808592.
- Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, et al. (1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1â€“2): 149â€“56. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
- Martindale DW, Wilson MD, Wang D, et al. (2000). "Comparative genomic sequence analysis of the Williams syndrome region (LIMK1-RFC2) of human chromosome 7q11.23". Mamm. Genome. 11 (10): 890â€“8. doi:10.1007/s003350010166. PMID 11003705.
- Zhang QH, Ye M, Wu XY, et al. (2001). "Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells". Genome Res. 10 (10): 1546â€“60. doi:10.1101/gr.140200. PMC 310934. PMID 11042152.
- Doyle JL, DeSilva U, Miller W, Green ED (2001). "Divergent human and mouse orthologs of a novel gene (WBSCR15/Wbscr15) reside within the genomic interval commonly deleted in Williams syndrome". Cytogenet. Cell Genet. 90 (3â€“4): 285â€“90. doi:10.1159/000056790. PMID 11124535.
- Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899â€“903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
- Brdicka T, Imrich M, AngelisovÃ¡ P, et al. (2003). "Non-T cell activation linker (NTAL): a transmembrane adaptor protein involved in immunoreceptor signaling". J. Exp. Med. 196 (12): 1617â€“26. doi:10.1084/jem.20021405. PMC 2196071. PMID 12486104.
- Hillier LW, Fulton RS, Fulton LA, et al. (2003). "The DNA sequence of human chromosome 7". Nature. 424 (6945): 157â€“64. Bibcode:2003Natur.424..157H. doi:10.1038/nature01782. PMID 12853948.
- Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40â€“5. doi:10.1038/ng1285. PMID 14702039.
- Koonpaew S, Janssen E, Zhu M, Zhang W (2004). "The importance of three membrane-distal tyrosines in the adaptor protein NTAL/LAB". J. Biol. Chem. 279 (12): 11229â€“35. doi:10.1074/jbc.M311394200. PMID 14722116.
- Tkaczyk C, Horejsi V, Iwaki S, et al. (2004). "NTAL phosphorylation is a pivotal link between the signaling cascades leading to human mast cell degranulation following Kit activation and Fc epsilon RI aggregation". Blood. 104 (1): 207â€“14. doi:10.1182/blood-2003-08-2769. PMID 15010370.
- Janssen E, Zhu M, Craven B, Zhang W (2004). "Linker for activation of B cells: a functional equivalent of a mutant linker for activation of T cells deficient in phospholipase C-gamma1 binding". J. Immunol. 172 (11): 6810â€“9. doi:10.4049/jimmunol.172.11.6810. PMID 15153499.
- Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121â€“7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.
- Tedoldi S, Paterson JC, Hansmann ML, et al. (2006). "Transmembrane adaptor molecules: a new category of lymphoid-cell markers". Blood. 107 (1): 213â€“21. doi:10.1182/blood-2005-06-2273. PMID 16160011.
- Rual JF, Venkatesan K, Hao T, et al. (2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173â€“8. Bibcode:2005Natur.437.1173R. doi:10.1038/nature04209. PMID 16189514.
|This article on a gene on human chromosome 7 is a stub. You can help Wikipedia by expanding it.|
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Linker for activation of T-cells family member 2 Provide feedback
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Brdicka T, Imrich M, Angelisova P, Brdickova N, Horvath O, Spicka J, Hilgert I, Luskova P, Draber P, Novak P, Engels N, Wienands J, Simeoni L, Osterreicher J, Aguado E, Malissen M, Schraven B, Horejsi V;, J Exp Med. 2002;196:1617-1626.: Non-T cell activation linker (NTAL): a transmembrane adaptor protein involved in immunoreceptor signaling. PUBMED:12486104 EPMC:12486104
This tab holds annotation information from the InterPro database.
InterPro entry IPR031428
The adaptor protein linker activator of T-cells 2 (LAT2), also called non-T-cell activation linker (NTAL), linker activator for B-cells (LAB) or Williams Beuren Syndrome critical region 5 (WBSCR5), is expressed in various myeloid and lymphoid cells [ PUBMED:16160011 ]. Given the wide expression pattern, it may modulate signalling in most types of leukocytes [ PUBMED:20643813 ]. It has been shown to be involved in immunoreceptor signaling [ PUBMED:12486104 ], B cell activation [ PUBMED:12514734 ], negative regulation of T cell activation [ PUBMED:17081783 ], and regulation of mast cell physiology [ PUBMED:25153696 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||immune response-regulating signaling pathway (GO:0002764)|
|B cell activation (GO:0042113)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Number in seed:||9|
|Number in full:||186|
|Average length of the domain:||122.50 aa|
|Average identity of full alignment:||45 %|
|Average coverage of the sequence by the domain:||75.83 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the LAT2 domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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