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1  structure 1036  species 0  interactions 2323  sequences 28  architectures

Family: LUC7 (PF03194)

Summary: LUC7 N_terminus

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

LUC7 N_terminus Provide feedback

This family contains the N terminal region of several LUC7 protein homologues and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein [1] with a role in splice site recognition [2]. The family also contains human and mouse LUC7 like (LUC7L) proteins [3] and human cisplatin resistance-associated overexpressed protein (CROP) [4].

Literature references

  1. Stevens SW, Ryan DE, Ge HY, Moore RE, Young MK, Lee TD, Abelson J; , Mol Cell 2002;9:31-44.: Composition and functional characterization of the yeast spliceosomal penta-snRNP. PUBMED:11804584 EPMC:11804584

  2. Fortes P, Bilbao-Cortes D, Fornerod M, Rigaut G, Raymond W, Seraphin B, Mattaj IW; , Genes Dev 1999;13:2425-2438.: Luc7p, a novel yeast U1 snRNP protein with a role in 5' splice site recognition. PUBMED:10500099 EPMC:10500099

  3. Tufarelli C, Frischauf AM, Hardison R, Flint J, Higgs DR; , Genomics 2001;71:307-314.: Characterization of a widely expressed gene (LUC7-LIKE; LUC7L) defining the centromeric boundary of the human alpha-globin domain. PUBMED:11170747 EPMC:11170747

  4. Nishii Y, Morishima M, Kakehi Y, Umehara K, Kioka N, Terano Y, Amachi T, Ueda K; , FEBS Lett 2000;465:153-156.: CROP/Luc7A, a novel serine/arginine-rich nuclear protein, isolated from cisplatin-resistant cell line. PUBMED:10631324 EPMC:10631324


This tab holds annotation information from the InterPro database.

InterPro entry IPR004882

This family consists of several Luc7 protein homologues that are restricted to eukaryotes. In budding yeast, Luc7 is an essential subunit of the yeast U1 snRNP, which forms the spliceosomal commitment complex with other proteins that targets pre-mRNA to the splicing pathway [PUBMED:17726058, PUBMED:11170747]. Its N-terminal zinc finger has been found to bind pre-mRNA [PUBMED:17726058]. This entry also contains human and mouse Luc7 like (LUC7L) proteins [PUBMED:10500099].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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...

View options

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
(73)
Full
(2323)
Representative proteomes UniProt
(3323)
NCBI
(4408)
Meta
(9)
RP15
(608)
RP35
(1182)
RP55
(1708)
RP75
(2012)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(73)
Full
(2323)
Representative proteomes UniProt
(3323)
NCBI
(4408)
Meta
(9)
RP15
(608)
RP35
(1182)
RP55
(1708)
RP75
(2012)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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.

  Seed
(73)
Full
(2323)
Representative proteomes UniProt
(3323)
NCBI
(4408)
Meta
(9)
RP15
(608)
RP35
(1182)
RP55
(1708)
RP75
(2012)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

Seed source: Pfam-B_2902 (release 6.5)
Previous IDs: DUF259;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 73
Number in full: 2323
Average length of the domain: 218.30 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 70.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 33.0 33.0
Trusted cut-off 33.2 33.2
Noise cut-off 32.4 32.7
Model length: 251
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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 LUC7 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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