UBAP1

Ubiquitin-associated protein 1 is a protein that in humans is encoded by the UBAP1 gene.[5]

UBAP1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1WGN, 4AE4
Identifiers
Aliases	UBAP1, NAG20, UAP, UBAP, UBAP-1, ubiquitin associated protein 1, SPG80
External IDs	OMIM: 609787 MGI: 2149543 HomoloGene: 9554 GeneCards: UBAP1
Gene location (Human) Chr. Chromosome 9 (human)[1] Band 9p13.3 Start 34,179,005 bp[1] End 34,252,523 bp[1]
Gene location (Mouse) Chr. Chromosome 4 (mouse)[2] Band 4|4 A5 Start 41,348,996 bp[2] End 41,390,525 bp[2]
RNA expression pattern More reference expression data
Gene ontology Molecular function • ubiquitin binding • GO:0001948 protein binding Cellular component • cytoplasm • cytosol • endosome • cell membrane • Golgi apparatus • ESCRT I complex • endosome membrane • host cell Biological process • protein transport • ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway • endosomal transport • GO:0019067 viral life cycle • GO:0046795 intracellular transport of virus Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	51271	67123
Ensembl	ENSG00000165006	ENSMUSG00000028437
UniProt	Q9NZ09	Q8BH48
RefSeq (mRNA)	NM_001171201 NM_001171202 NM_001171203 NM_001171204 NM_016525	NM_001290454 NM_023305 NM_001355508 NM_001355509
RefSeq (protein)	NP_001164672 NP_001164673 NP_001164674 NP_001164675 NP_057609	NP_001277383 NP_075794 NP_001342437 NP_001342438
Location (UCSC)	Chr 9: 34.18 – 34.25 Mb	Chr 4: 41.35 – 41.39 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

This gene is a member of the UBA domain family, whose members include proteins having connections to ubiquitin and the ubiquitination pathway. The ubiquitin associated domain is thought to be a non-covalent ubiquitin binding domain consisting of a compact three helix bundle. This particular protein originates from a gene locus in a refined region on chromosome 9 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). Taking into account its cytogenetic location, this UBA domain family member is being studies as a putative target for mutation in nasopharyngeal carcinomas.[5] Truncating Mutations in UBAP1 Cause Hereditary Spastic Paraplegia.[6]

Model organisms

Ubap1 knockout mouse phenotype

Characteristic	Phenotype
Homozygote viability	Abnormal
Recessive lethal study	Abnormal
Fertility	Normal
Body weight	Normal
Anxiety	Normal
Neurological assessment	Normal
Grip strength	Normal
Hot plate	Normal
Dysmorphology	Normal
Indirect calorimetry	Normal
Glucose tolerance test	Normal
Auditory brainstem response	Normal
DEXA	Normal
Radiography	Normal
Body temperature	Normal
Eye morphology	Normal
Clinical chemistry	Normal
Plasma immunoglobulins	Normal
Haematology	Normal
Peripheral blood lymphocytes	Normal
Micronucleus test	Normal
Heart weight	Normal
Brain histopathology	Normal
Salmonella infection	Normal[7]
Citrobacter infection	Normal[8]
All tests and analysis from[9][10]

Model organisms have been used in the study of UBAP1 function. A conditional knockout mouse line, called Ubap1^{tm1a(EUCOMM)Wtsi}[11][12] was generated as part of the International Knockout Mouse Consortium program — a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists — at the Wellcome Trust Sanger Institute.[13][14][15]

Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion.[9][16] Twenty five tests were carried out and two phenotypes were reported. Fewer homozygous mutant embryos were identified during gestation than predicted, and none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice; no significant abnormalities were observed in these animals.[9]

References

1. GRCh38: Ensembl release 89: ENSG00000165006 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000028437 - Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. "Entrez Gene: UBAP1 ubiquitin associated protein 1".
6. Farazi Fard MA, Rebelo AP, Buglo E, Nemati H, Dastsooz H, Gehweiler I, et al. (April 2019). "Truncating Mutations in UBAP1 Cause Hereditary Spastic Paraplegia". American Journal of Human Genetics. 104 (4): 767–773. doi:10.1016/j.ajhg.2019.03.001. PMC 6451742. PMID 30929741.
7. "Salmonella infection data for Ubap1". Wellcome Trust Sanger Institute.
8. "Citrobacter infection data for Ubap1". Wellcome Trust Sanger Institute.
9. Gerdin AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta Ophthalmologica. 88 (S248): 0. doi:10.1111/j.1755-3768.2010.4142.x.
10. Mouse Resources Portal, Wellcome Trust Sanger Institute.
11. "International Knockout Mouse Consortium".
12. "Mouse Genome Informatics".
13. Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, et al. (June 2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337–42. doi:10.1038/nature10163. PMC 3572410. PMID 21677750.
14. Dolgin E (June 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi:10.1038/474262a. PMID 21677718.
15. Collins FS, Rossant J, Wurst W (January 2007). "A mouse for all reasons". Cell. 128 (1): 9–13. doi:10.1016/j.cell.2006.12.018. PMID 17218247.
16. van der Weyden L, White JK, Adams DJ, Logan DW (June 2011). "The mouse genetics toolkit: revealing function and mechanism". Genome Biology. 12 (6): 224. doi:10.1186/gb-2011-12-6-224. PMC 3218837. PMID 21722353.

Further reading

• Maruyama K, Sugano S (January 1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene. 138 (1–2): 171–4. doi:10.1016/0378-1119(94)90802-8. PMID 8125298.
• Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S (October 1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene. 200 (1–2): 149–56. doi:10.1016/S0378-1119(97)00411-3. PMID 9373149.
• Hartley JL, Temple GF, Brasch MA (November 2000). "DNA cloning using in vitro site-specific recombination". Genome Research. 10 (11): 1788–95. doi:10.1101/gr.143000. PMC 310948. PMID 11076863.
• Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, et al. (March 2001). "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs". Genome Research. 11 (3): 422–35. doi:10.1101/gr.GR1547R. PMC 311072. PMID 11230166.
• Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S (September 2000). "Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing". EMBO Reports. 1 (3): 287–92. doi:10.1093/embo-reports/kvd058. PMC 1083732. PMID 11256614.
• Qian J, Yang J, Zhang X, Zhang B, Wang J, Zhou M, et al. (October 2001). "Isolation and characterization of a novel cDNA, UBAP1, derived from the tumor suppressor locus in human chromosome 9p21-22". Journal of Cancer Research and Clinical Oncology. 127 (10): 613–8. doi:10.1007/s004320100252. PMID 11599797.
• Qian J, Zhang XH, Yang JB, Wang JR, Zhang BC, Tang K, Li GY (2001). "Cloning and Expression Analysis of a Novel Gene, UBAP1, Possibly Involved in Ubiquitin Pathway". Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao Acta Biochimica et Biophysica Sinica. 33 (2): 147–152. PMID 12050802.
• Qian J, Zhang XM, Li XL, Wang JR, Li WF, Wang R, Li GY (March 2002). "[Identification of digital differential expression patterns of a novel human gene (UBAP1) by an expressed sequence tag strategy]". AI Zheng = Aizheng = Chinese Journal of Cancer. 21 (3): 225–8. PMID 12451983.
• Wiemann S, Arlt D, Huber W, Wellenreuther R, Schleeger S, Mehrle A, et al. (October 2004). "From ORFeome to biology: a functional genomics pipeline". Genome Research. 14 (10B): 2136–44. doi:10.1101/gr.2576704. PMC 528930. PMID 15489336.
• Xiao B, Fan S, Zeng Z, Xiong W, Cao L, Yang Y, et al. (May 2006). "Purification of novel UBAP1 protein and its decreased expression on nasopharyngeal carcinoma tissue microarray". Protein Expression and Purification. 47 (1): 60–7. doi:10.1016/j.pep.2005.08.026. PMID 16226037.
• Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, et al. (January 2006). "The LIFEdb database in 2006". Nucleic Acids Research. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501. PMID 16381901.