Summary: Lysine-rich CEACAM1 co-isolated protein family
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Lysine-rich CEACAM1 co-isolated protein family Provide feedback
LYRIC is a family of proteins found in eukaryotes. It is a type-1b membrane protein with a single transmembrane domain and localises to the endoplasmic reticulum and the nuclear envelope. It is also found in the nucleolus, suggesting functional relationships between these two cellular compartments [1]. It is found to be colocalised with tight junction proteins ZO-1 and occludin in polarised epithelial cells, suggesting that LYRIC is part of the tight junction complex [2]. LYRIC has been shown to promote tumour cell migration and invasion by activating the transcription factor NF-kappaB [3].
Literature references
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Sutherland HG, Lam YW, Briers S, Lamond AI, Bickmore WA;, Exp Cell Res. 2004;294:94-105.: 3D3/lyric: a novel transmembrane protein of the endoplasmic reticulum and nuclear envelope, which is also present in the nucleolus. PUBMED:14980505 EPMC:14980505
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Britt DE, Yang DF, Yang DQ, Flanagan D, Callanan H, Lim YP, Lin SH, Hixson DC;, Exp Cell Res. 2004;300:134-148.: Identification of a novel protein, LYRIC, localized to tight junctions of polarized epithelial cells. PUBMED:15383321 EPMC:15383321
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Ash SC, Yang DQ, Britt DE;, Biochem Biophys Res Commun. 2008;371:333-338.: LYRIC/AEG-1 overexpression modulates BCCIPalpha protein levels in prostate tumor cells. PUBMED:18440304 EPMC:18440304
Internal database links
SCOOP: | MAP17 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR031402
LYRIC (Lysine-rich CEACAM1 co-isolated protein), also known as Astrocyte-elevated gene-1 (AEG-1), is a type-1b membrane protein with a single transmembrane domain and localises to the endoplasmic reticulum and the nuclear envelope. It is also found in the nucleolus, suggesting functional relationships between these two cellular compartments [PUBMED:14980505]. It is found to be colocalised with tight junction proteins ZO-1 and occludin in polarised epithelial cells, suggesting that LYRIC is part of the tight junction complex [PUBMED:15383321]. LYRIC has been shown to promote angiogenesis [PUBMED:19940250] and tumour cell migration and invasion by activating the transcription factor NF-kappaB [PUBMED:16452207, PUBMED:18440304, PUBMED:17704808].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Biological process | positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123) |
positive regulation of angiogenesis (GO:0045766) | |
negative regulation of apoptotic process (GO:0043066) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Alignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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.
Seed (12) |
Full (411) |
Representative proteomes | UniProt (670) |
NCBI (1587) |
Meta (0) |
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RP15 (17) |
RP35 (77) |
RP55 (248) |
RP75 (400) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (12) |
Full (411) |
Representative proteomes | UniProt (670) |
NCBI (1587) |
Meta (0) |
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RP15 (17) |
RP35 (77) |
RP55 (248) |
RP75 (400) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
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.
Note: You can also download the data file for the tree.
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.
Curation
Seed source: | Jackhmmer:Q86UE4 |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Eberhardt R |
Number in seed: | 12 |
Number in full: | 411 |
Average length of the domain: | 285.10 aa |
Average identity of full alignment: | 41 % |
Average coverage of the sequence by the domain: | 73.76 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 424 | ||||||||||||
Family (HMM) version: | 6 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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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 adjacent tab. More...
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Structures
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 LYRIC domain has been found. There are 5 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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