Summary: Fanconi anaemia group A protein

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FANCA Edit Wikipedia article

Fanconi anemia, complementation group A

Identifiers

Symbols

FANCA; FA; FA-H; FA1; FAA; FACA; FAH; FANCH

External IDs

OMIM: 607139 MGI: 1341823 HomoloGene: 108 GeneCards: FANCA Gene

Gene Ontology
Molecular function	protein binding
Cellular component	nucleus nucleoplasm cytoplasm Fanconi anaemia nuclear complex
Biological process	DNA repair protein complex assembly male meiosis male gonad development female gonad development regulation of cell proliferation
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 16:
89.8 89.88 Mb

Chr 8:
125.79 125.84 Mb

PubMed search

[1]

[2]

Fanconi anemia, complementation group A, also known as FANCA, is a protein which in humans is encoded by the FANCA gene.^[1]

[edit] Function

The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, and FANCL. The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group A. Alternative splicing results in multiple transcript variants encoding different isoforms.^[1]

Fanconi anaemia group A protein

Identifiers

Symbol

Fanconi_A

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

[edit] Clinical significance

Mutations in this gene are the most common cause of Fanconi anemia.^[1]

[edit] Interactions

FANCA has been shown to interact with ERCC4,^[2] IKK2,^[3] Fanconi anemia, complementation group C,^[3]^[4]^[5]^[6]^[7]^[8]^[9]^[10] FANCG,^[4]^[7]^[8]^[9]^[11]^[3]^[12]^[10]^[13]^[14]^[15]^[16]^[17]^[18]^[19]^[20]^[21]^[22] FANCF,^[5]^[9]^[23] FANCE,^[9]^[10]^[21]^[24] BRCA1,^[25] SNX5,^[26] SPTAN1,^[2]^[6]^[27] SMARCA4^[28]^[29] and CHUK.^[3]^[29]

[edit] References

^ ^a ^b ^c "Entrez Gene: FANCA Fanconi anemia, complementation group A". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2175.
^ ^a ^b Sridharan, Deepa; Brown Monique, Lambert W Clark, McMahon Laura W, Lambert Muriel W (March 2003). "Nonerythroid alphaII spectrin is required for recruitment of FANCA and XPF to nuclear foci induced by DNA interstrand cross-links". J. Cell. Sci. (England) 116 (Pt 5): 82335. DOI:10.1242/jcs.00294. ISSN 0021-9533. PMID 12571280.
^ ^a ^b ^c ^d Otsuki, Tetsuya; Young David B, Sasaki Dennis T, Pando Matthew P, Li Jianwu, Manning Anthony, Hoekstra Merl, Hoatlin Maureen E, Mercurio Frank, Liu Johnson M (2002). "Fanconi anemia protein complex is a novel target of the IKK signalsome". J. Cell. Biochem. (United States) 86 (4): 61323. DOI:10.1002/jcb.10270. ISSN 0730-2312. PMID 12210728.
^ ^a ^b Garcia-Higuera, I; Kuang Y, Näf D, Wasik J, D'Andrea A D (July 1999). "Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex". Mol. Cell. Biol. (UNITED STATES) 19 (7): 486673. ISSN 0270-7306. PMC 84285. PMID 10373536. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=84285.
^ ^a ^b de Winter, J P; van der Weel L, de Groot J, Stone S, Waisfisz Q, Arwert F, Scheper R J, Kruyt F A, Hoatlin M E, Joenje H (November 2000). "The Fanconi anemia protein FANCF forms a nuclear complex with FANCA, FANCC and FANCG". Hum. Mol. Genet. (ENGLAND) 9 (18): 266574. DOI:10.1093/hmg/9.18.2665. ISSN 0964-6906. PMID 11063725.
^ ^a ^b McMahon, L W; Walsh C E, Lambert M W (November 1999). "Human alpha spectrin II and the Fanconi anemia proteins FANCA and FANCC interact to form a nuclear complex". J. Biol. Chem. (UNITED STATES) 274 (46): 329048. DOI:10.1074/jbc.274.46.32904. ISSN 0021-9258. PMID 10551855.
^ ^a ^b Reuter, T; Herterich S, Bernhard O, Hoehn H, Gross H J (January 2000). "Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system". Blood (UNITED STATES) 95 (2): 71920. ISSN 0006-4971. PMID 10627486.
^ ^a ^b Thomashevski, Andrei; High Anthony A, Drozd Mary, Shabanowitz Jeffrey, Hunt Donald F, Grant Patrick A, Kupfer Gary M (June 2004). "The Fanconi anemia core complex forms four complexes of different sizes in different subcellular compartments". J. Biol. Chem. (United States) 279 (25): 262019. DOI:10.1074/jbc.M400091200. ISSN 0021-9258. PMID 15082718.
^ ^a ^b ^c ^d Meetei, Amom Ruhikanta; de Winter Johan P, Medhurst Annette L, Wallisch Michael, Waisfisz Quinten, van de Vrugt Henri J, Oostra Anneke B, Yan Zhijiang, Ling Chen, Bishop Colin E, Hoatlin Maureen E, Joenje Hans, Wang Weidong (October 2003). "A novel ubiquitin ligase is deficient in Fanconi anemia". Nat. Genet. (United States) 35 (2): 16570. DOI:10.1038/ng1241. ISSN 1061-4036. PMID 12973351.
^ ^a ^b ^c Taniguchi, Toshiyasu; D'Andrea Alan D (October 2002). "The Fanconi anemia protein, FANCE, promotes the nuclear accumulation of FANCC". Blood (United States) 100 (7): 245762. DOI:10.1182/blood-2002-03-0860. ISSN 0006-4971. PMID 12239156.
^ Rual, Jean-François; Venkatesan Kavitha, Hao Tong, Hirozane-Kishikawa Tomoko, Dricot Amélie, Li Ning, Berriz Gabriel F, Gibbons Francis D, Dreze Matija, Ayivi-Guedehoussou Nono, Klitgord Niels, Simon Christophe, Boxem Mike, Milstein Stuart, Rosenberg Jennifer, Goldberg Debra S, Zhang Lan V, Wong Sharyl L, Franklin Giovanni, Li Siming, Albala Joanna S, Lim Janghoo, Fraughton Carlene, Llamosas Estelle, Cevik Sebiha, Bex Camille, Lamesch Philippe, Sikorski Robert S, Vandenhaute Jean, Zoghbi Huda Y, Smolyar Alex, Bosak Stephanie, Sequerra Reynaldo, Doucette-Stamm Lynn, Cusick Michael E, Hill David E, Roth Frederick P, Vidal Marc (October 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature (England) 437 (7062): 11738. DOI:10.1038/nature04209. PMID 16189514.
^ Park, Su-Jung; Ciccone Samantha L M, Beck Brian D, Hwang Byounghoon, Freie Brian, Clapp D Wade, Lee Suk-Hee (July 2004). "Oxidative stress/damage induces multimerization and interaction of Fanconi anemia proteins". J. Biol. Chem. (United States) 279 (29): 300539. DOI:10.1074/jbc.M403527200. ISSN 0021-9258. PMID 15138265.
^ van de Vrugt, Henri J; Koomen Mireille, Berns Mariska A D, de Vries Yne, Rooimans Martin A, van der Weel Laura, Blom Eric, de Groot Jan, Schepers Rik J, Stone Stacie, Hoatlin Maureen E, Cheng Ngan Ching, Joenje Hans, Arwert Fré (March 2002). "Characterization, expression and complex formation of the murine Fanconi anaemia gene product Fancg". Genes Cells (England) 7 (3): 33342. DOI:10.1046/j.1365-2443.2002.00518.x. ISSN 1356-9597. PMID 11918676.
^ Yagasaki, H; Adachi D, Oda T, Garcia-Higuera I, Tetteh N, D'Andrea A D, Futaki M, Asano S, Yamashita T (December 2001). "A cytoplasmic serine protein kinase binds and may regulate the Fanconi anemia protein FANCA". Blood (United States) 98 (13): 36507. DOI:10.1182/blood.V98.13.3650. ISSN 0006-4971. PMID 11739169.
^ Gordon, Susan M; Buchwald Manuel (July 2003). "Fanconi anemia protein complex: mapping protein interactions in the yeast 2- and 3-hybrid systems". Blood (United States) 102 (1): 13641. DOI:10.1182/blood-2002-11-3517. ISSN 0006-4971. PMID 12649160.
^ Huber, P A; Medhurst A L, Youssoufian H, Mathew C G (February 2000). "Investigation of Fanconi anemia protein interactions by yeast two-hybrid analysis". Biochem. Biophys. Res. Commun. (UNITED STATES) 268 (1): 737. DOI:10.1006/bbrc.1999.2055. ISSN 0006-291X. PMID 10652215.
^ Kruyt, F A; Abou-Zahr F, Mok H, Youssoufian H (November 1999). "Resistance to mitomycin C requires direct interaction between the Fanconi anemia proteins FANCA and FANCG in the nucleus through an arginine-rich domain". J. Biol. Chem. (UNITED STATES) 274 (48): 342128. DOI:10.1074/jbc.274.48.34212. ISSN 0021-9258. PMID 10567393.
^ Blom, Eric; van de Vrugt Henri J, de Vries Yne, de Winter Johan P, Arwert Fré, Joenje Hans (January 2004). "Multiple TPR motifs characterize the Fanconi anemia FANCG protein". DNA Repair (Amst.) (Netherlands) 3 (1): 7784. DOI:10.1016/j.dnarep.2003.09.007. ISSN 1568-7864. PMID 14697762.
^ Kuang, Y; Garcia-Higuera I, Moran A, Mondoux M, Digweed M, D'Andrea A D (September 2000). "Carboxy terminal region of the Fanconi anemia protein, FANCG/XRCC9, is required for functional activity". Blood (UNITED STATES) 96 (5): 162532. ISSN 0006-4971. PMID 10961856.
^ Waisfisz, Q; de Winter J P, Kruyt F A, de Groot J, van der Weel L, Dijkmans L M, Zhi Y, Arwert F, Scheper R J, Youssoufian H, Hoatlin M E, Joenje H (August 1999). "A physical complex of the Fanconi anemia proteins FANCG/XRCC9 and FANCA". Proc. Natl. Acad. Sci. U.S.A. (UNITED STATES) 96 (18): 103205. DOI:10.1073/pnas.96.18.10320. ISSN 0027-8424. PMC 17886. PMID 10468606. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=17886.
^ ^a ^b Medhurst, A L; Huber P A, Waisfisz Q, de Winter J P, Mathew C G (February 2001). "Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway". Hum. Mol. Genet. (England) 10 (4): 4239. DOI:10.1093/hmg/10.4.423. ISSN 0964-6906. PMID 11157805.
^ Garcia-Higuera, I; Kuang Y, Denham J, D'Andrea A D (November 2000). "The fanconi anemia proteins FANCA and FANCG stabilize each other and promote the nuclear accumulation of the Fanconi anemia complex". Blood (UNITED STATES) 96 (9): 322430. ISSN 0006-4971. PMID 11050007.
^ Léveillé, France; Blom Eric, Medhurst Annette L, Bier Patrick, Laghmani El Houari, Johnson Mark, Rooimans Martin A, Sobeck Alexandra, Waisfisz Quinten, Arwert Fré, Patel K J, Hoatlin Maureen E, Joenje Hans, de Winter Johan P (September 2004). "The Fanconi anemia gene product FANCF is a flexible adaptor protein". J. Biol. Chem. (United States) 279 (38): 3942130. DOI:10.1074/jbc.M407034200. ISSN 0021-9258. PMID 15262960.
^ Pace, Paul; Johnson Mark, Tan Wu Meng, Mosedale Georgina, Sng Chelvin, Hoatlin Maureen, de Winter Johan, Joenje Hans, Gergely Fanni, Patel K J (July 2002). "FANCE: the link between Fanconi anaemia complex assembly and activity". EMBO J. (England) 21 (13): 341423. DOI:10.1093/emboj/cdf355. ISSN 0261-4189. PMC 125396. PMID 12093742. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=125396.
^ Folias, Alexandra; Matkovic Mara, Bruun Donald, Reid Sonja, Hejna James, Grompe Markus, D'Andrea Alan, Moses Robb (October 2002). "BRCA1 interacts directly with the Fanconi anemia protein FANCA". Hum. Mol. Genet. (England) 11 (21): 25917. DOI:10.1093/hmg/11.21.2591. ISSN 0964-6906. PMID 12354784.
^ Otsuki, T; Kajigaya S, Ozawa K, Liu J M (November 1999). "SNX5, a new member of the sorting nexin family, binds to the Fanconi anemia complementation group A protein". Biochem. Biophys. Res. Commun. (UNITED STATES) 265 (3): 6305. DOI:10.1006/bbrc.1999.1731. ISSN 0006-291X. PMID 10600472.
^ McMahon, L W; Sangerman J, Goodman S R, Kumaresan K, Lambert M W (June 2001). "Human alpha spectrin II and the FANCA, FANCC, and FANCG proteins bind to DNA containing psoralen interstrand cross-links". Biochemistry (United States) 40 (24): 702534. DOI:10.1021/bi002917g. ISSN 0006-2960. PMID 11401546.
^ Otsuki, T; Furukawa Y, Ikeda K, Endo H, Yamashita T, Shinohara A, Iwamatsu A, Ozawa K, Liu J M (November 2001). "Fanconi anemia protein, FANCA, associates with BRG1, a component of the human SWI/SNF complex". Hum. Mol. Genet. (England) 10 (23): 265160. DOI:10.1093/hmg/10.23.2651. ISSN 0964-6906. PMID 11726552.
^ ^a ^b Reuter, Tanja Y; Medhurst Annette L, Waisfisz Quinten, Zhi Yu, Herterich Sabine, Hoehn Holger, Gross Hans J, Joenje Hans, Hoatlin Maureen E, Mathew Christopher G, Huber Pia A J (October 2003). "Yeast two-hybrid screens imply involvement of Fanconi anemia proteins in transcription regulation, cell signaling, oxidative metabolism, and cellular transport". Exp. Cell Res. (United States) 289 (2): 21121. DOI:10.1016/S0014-4827(03)00261-1. ISSN 0014-4827. PMID 14499622.

[edit] Further reading

Marmo E (1976). "[Beta-adrenolytic agents in the treatment of hypertension]". La Clinica terapeutica 74 (3): 20929. PMID 6186.
Pronk JC, Gibson RA, Savoia A, et al. (1995). "Localisation of the Fanconi anaemia complementation group A gene to chromosome 16q24.3.". Nat. Genet. 11 (3): 33840. DOI:10.1038/ng1195-338. PMID 7581462.
Gschwend M, Levran O, Kruglyak L, et al. (1996). "A locus for Fanconi anemia on 16q determined by homozygosity mapping.". Am. J. Hum. Genet. 59 (2): 37784. PMC 1914713. PMID 8755924. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1914713.
Lo Ten Foe JR, Rooimans MA, Bosnoyan-Collins L, et al. (1996). "Expression cloning of a cDNA for the major Fanconi anaemia gene, FAA.". Nat. Genet. 14 (3): 3203. DOI:10.1038/ng1196-320. PMID 8896563.
Apostolou, Sinoula; Whitmore, Scott A.; Crawford, Joanna; Lennon, Gregory; Sutherland, Grant R.; Callen, David F.; Lanzano, Leonarda; Savino, Maria et al. (1996). "Positional cloning of the Fanconi anaemia group A gene. The Fanconi anaemia/breast cancer consortium.". Nat. Genet. 14 (3): 3248. DOI:10.1038/ng1196-324. PMID 8896564.
Ianzano L, D'Apolito M, Centra M, et al. (1997). "The genomic organization of the Fanconi anemia group A (FAA) gene.". Genomics 41 (3): 30914. DOI:10.1006/geno.1997.4675. PMID 9169126.
Levran O, Erlich T, Magdalena N, et al. (1998). "Sequence variation in the Fanconi anemia gene FAA.". Proc. Natl. Acad. Sci. U.S.A. 94 (24): 130516. DOI:10.1073/pnas.94.24.13051. PMC 24261. PMID 9371798. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=24261.
Joenje H, Oostra AB, Wijker M, et al. (1997). "Evidence for at least eight Fanconi anemia genes.". Am. J. Hum. Genet. 61 (4): 9404. DOI:10.1086/514881. PMC 1715980. PMID 9382107. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1715980.
Kupfer GM, Näf D, Suliman A, et al. (1997). "The Fanconi anaemia proteins, FAA and FAC, interact to form a nuclear complex.". Nat. Genet. 17 (4): 48790. DOI:10.1038/ng1297-487. PMID 9398857.
Savino M, Ianzano L, Strippoli P, et al. (1998). "Mutations of the Fanconi anemia group A gene (FAA) in Italian patients.". Am. J. Hum. Genet. 61 (6): 124653. DOI:10.1086/301632. PMC 1716093. PMID 9399890. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1716093.
Levran O, Doggett NA, Auerbach AD (1998). "Identification of Alu-mediated deletions in the Fanconi anemia gene FAA.". Hum. Mutat. 12 (3): 14552. DOI:10.1002/(SICI)1098-1004(1998)12:3<145::AID-HUMU2>3.0.CO;2-G. PMID 9711872.
Centra M, Memeo E, d'Apolito M, et al. (1998). "Fine exon-intron structure of the Fanconi anemia group A (FAA) gene and characterization of two genomic deletions.". Genomics 51 (3): 4637. DOI:10.1006/geno.1998.5353. PMID 9721219.
Näf D, Kupfer GM, Suliman A, et al. (1998). "Functional activity of the fanconi anemia protein FAA requires FAC binding and nuclear localization.". Mol. Cell. Biol. 18 (10): 595260. PMC 109181. PMID 9742112. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=109181.
Yamashita T, Kupfer GM, Naf D, et al. (1998). "The fanconi anemia pathway requires FAA phosphorylation and FAA/FAC nuclear accumulation.". Proc. Natl. Acad. Sci. U.S.A. 95 (22): 1308590. DOI:10.1073/pnas.95.22.13085. PMC 23717. PMID 9789045. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=23717.
Nakamura A, Matsuura S, Tauchi H, et al. (1999). "Four novel mutations of the Fanconi anemia group A gene (FAA) in Japanese patients.". J. Hum. Genet. 44 (1): 4851. DOI:10.1007/s100380050106. PMID 9929978.
Wijker M, Morgan NV, Herterich S, et al. (1999). "Heterogeneous spectrum of mutations in the Fanconi anaemia group A gene.". Eur. J. Hum. Genet. 7 (1): 529. DOI:10.1038/sj.ejhg.5200248. PMID 10094191.
Kupfer G, Naf D, Garcia-Higuera I, et al. (1999). "A patient-derived mutant form of the Fanconi anemia protein, FANCA, is defective in nuclear accumulation.". Exp. Hematol. 27 (4): 58793. DOI:10.1016/S0301-472X(99)00022-3. PMID 10210316.
Garcia-Higuera I, Kuang Y, Näf D, et al. (1999). "Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex.". Mol. Cell. Biol. 19 (7): 486673. PMC 84285. PMID 10373536. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=84285.
Jelesko JG, Harper R, Furuya M, Gruissem W (1999). "Rare germinal unequal crossing-over leading to recombinant gene formation and gene duplication in Arabidopsis thaliana.". Proc. Natl. Acad. Sci. U.S.A. 96 (18): 103027. DOI:10.1073/pnas.96.18.10302. PMC 17883. PMID 10468603. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=17883.
Waisfisz Q, de Winter JP, Kruyt FA, et al. (1999). "A physical complex of the Fanconi anemia proteins FANCG/XRCC9 and FANCA.". Proc. Natl. Acad. Sci. U.S.A. 96 (18): 103205. DOI:10.1073/pnas.96.18.10320. PMC 17886. PMID 10468606. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=17886.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Fanconi anaemia group A protein Provide feedback

No Pfam abstract.

External database links

PANDIT:	PF03511
Pseudofam:	PF03511
SYSTERS:	Fanconi_A

This tab holds annotation information from the InterPro database.

InterPro entry IPR003516

Fanconi anaemia (FA) [PUBMED:1641028, PUBMED:8490620, PUBMED:7929819] is a recessive inherited disease characterised by defective DNA repair. FA cells are sensitive to DNA cross-linking agents that cause chromosomal instability and cell death. The disease is manifested clinically by progressive pancytopenia, variable physical anomalies, and predisposition to malignancy [PUBMED:7929819]. Four complementation groups have been identified, designated A to D. The FA group A gene (FAA) has been cloned [PUBMED:9169126], but its function remains to be elucidated.

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	Seed (2)	Full (47)	Representative proteomes				NCBI (44)	Meta (0)
	Seed (2)	Full (47)	RP15 (1)	RP35 (2)	RP55 (7)	RP75 (22)	NCBI (44)	Meta (0)
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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 (2)	Full (47)	Representative proteomes				NCBI (44)	Meta (0)
	Seed (2)	Full (47)	RP15 (1)	RP35 (2)	RP55 (7)	RP75 (22)	NCBI (44)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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:

PRINTS

Previous IDs:

Fanconia;

Type:

Family

Author:

Griffiths-Jones SR

Number in seed:

2

Number in full:

47

Average length of the domain:

61.90 aa

Average identity of full alignment:

56 %

Average coverage of the sequence by the domain:

5.08 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.9	20.9
Trusted cut-off	21.0	32.3
Noise cut-off	19.5	19.6

Model length:

64

Family (HMM) version:

9

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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...

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:

superkingdom
kingdom
phylum
class
order
family
genus
species

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".

Sub-species

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.

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Species trees

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.

Interactive tree

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
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

Loading...

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.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Fanconi_A (PF03511)

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