Summary: XAP5, circadian clock regulator
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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.
XAP5, circadian clock regulator Provide feedback
This protein is found in a wide range of eukaryotes. It is a nuclear protein previously suggested to be DNA binding [1,2] but recent studies suggest that they play a role in the spliceosome complex [3]. In plants, this family is essential for correct circadian clock functioning by acting as a light-quality regulator coordinating the activities of blue and red light signalling pathways during plant growth - inhibiting growth in red light but promoting growth in blue light [4].
Literature references
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Mazzarella R, Pengue G, Yoon J, Jones J, Schlessinger D; , Genomics 1997;45:216-219.: Differential expression of XAP5, a candidate disease gene. PUBMED:9339379 EPMC:9339379
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Sedlacek Z, Munstermann E, Dhorne-Pollet S, Otto C, Bock D, Schutz G, Poustka A; , Genomics 1999;61:125-132.: Human and mouse XAP-5 and XAP-5-like (X5L) genes: identification of an ancient functional retroposon differentially expressed in testis. PUBMED:10534398 EPMC:10534398
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Lee YR, Khan K, Armfield-Uhas K, Srikanth S, Thompson NA, Pardo M, Yu L, Norris JW, Peng Y, Gripp KW, Aleck KA, Li C, Spence E, Choi TI, Kwon SJ, Park HM, Yu D, Do Heo W, Mooney MR, Baig SM, Wentzensen IM, Telegrafi A, McWalter K, Moreland T, Roadhouse C, Ramsey K, Lyons MJ, Skinner C, Alexov E, Katsanis N, Stevenson RE, Choudhary JS, Adams DJ, Kim CH, Davis EE, Schwartz CE;, Nat Commun. 2020;11:3698.: Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy. PUBMED:32703943 EPMC:32703943
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Martin-Tryon EL, Harmer SL;, Plant Cell. 2008;20:1244-1259.: XAP5 CIRCADIAN TIMEKEEPER coordinates light signals for proper timing of photomorphogenesis and the circadian clock in Arabidopsis. PUBMED:18515502 EPMC:18515502
Internal database links
SCOOP: | NDUF_B6 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR007005
These proteins are found in a wide range of eukaryotes. They are nuclear proteins, suggested to play a role in the spliceosome complex [ PUBMED:32703943 ]. XAP5 from Arabidopsis thaliana has been shown to be involved in light regulation of the circadian clock and photomorphogenesis [ PUBMED:18515502 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | nucleus (GO:0005634) |
Domain organisation
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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 and the UniProtKB 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 (91) |
Full (1574) |
Representative proteomes | UniProt (2775) |
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RP15 (334) |
RP35 (758) |
RP55 (1257) |
RP75 (1662) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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Seed (91) |
Full (1574) |
Representative proteomes | UniProt (2775) |
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RP15 (334) |
RP35 (758) |
RP55 (1257) |
RP75 (1662) |
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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: | Pfam-B_4702 (release 7.6) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bateman A |
Number in seed: | 91 |
Number in full: | 1574 |
Average length of the domain: | 239.70 aa |
Average identity of full alignment: | 42 % |
Average coverage of the sequence by the domain: | 68.98 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 254 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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