ALFRED: allele frequency database

The ALlele FREquency Database
ALFRED is a resource of gene frequency data on human populations
supported by the U. S. National Science Foundation.

ALFRED detailed record information

Locus Information

Name	ALFRED UID	Locus Symbol	Chromosome	Band Position
Plasminogen activator, tissue	LO000193N	PLAT	8	8p11.2

Synonyms:
Sites List: See Sites List
External Resources: Entrez Gene Locus Information OMIM description GenBank sequence GenBank sequence PharmGKB Gene Information Genopedia (HuGE Navigator)
References: See References
Locus Description: This gene encodes tissue-type plasminogen activator (t-PA), a secreted serine protease which converts the inactive proenzyme plasminogen to plasmin, a proteinase associated with processes such as fibrinolysis and tissue remodeling (Benham et al., 1984) [PubMed ID: 6100560]. The PLAT gene spans 36,594 bp located on the short arm of chromosome 8 at 8p11.2 (Degen et al., 1986) [PubMed ID: 3009482]. The gene is comprised of 14 exons, ranging in size from 43 to 914 bp. In the adult brain, t-PA is highly expressed in the hippocampus, amygdala, cerebellum, and hypothalamus. These regions regulate many biological functions, including learning and memory (hippocampus), emotion and fear (amygdala), motor coordination (cerebellum), and autonomic, endocrine, and visceral function (hypothalamus). Tsirka et al. (1995) [PubMed ID: 7566088] identified that t-PA plays a role in neuronal degeneration (Alzheimer's disease) and seizure. The gene and 5' flanking region contain 28 copies of Alu repetitive DNA sequence (Degen et al., 1986) [PubMed ID: 3009482] including a polymorphic Alu element referred to as TPA25 in much of the literature.
Sites within this locus ordered by their chromosomal position in the 37.3 NCBI build:

Site Name (Navigates to ALFRED description)	dbSNP rs# (Navigates to dbSNP reference page)	Chr-Position	# Populations typed
rs4581040	rs4581040	42032026	50
rs1136159	rs1136159	42036577	50
TPA25 Alu insertion	rs4646972	42039905	188
rs2070713	rs2070713	42045655	51
rs8178732	rs8178732	42049319	50
rs8178730	rs8178730	42049856	50
C___2533651_10	rs732612	42168525	57
2-site haplotype ((CA) repeat 1, Alu)			30
2-site haplotype ((CA) repeat 2, Alu)			30

References:
- Benham FJ, Spurr N, Povey S, Brinton BT, Goodfellow PN, Solomon E, Harris TJ. "Assignment of tissue-type plasminogen activator to chromosome 8 in man and identification of a common restriction length polymorphism within the gene". Mol. Biol. Med. 2:251-9. (1984) Online citation.

- Degen SJ, Rajput B, Reich E. "The human tissue plasminogen activator gene". J. Biol. Chem. 261:6972-85. (1986) Online citation.

- Tishkoff SA, Pakstis AJ, Stoneking M, Kidd JR, Destro-Bisol G, Sanjantila A, Lu RB, Deinard AS, Sirugo G, Jenkins T, Kidd KK, Clark AG. "Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: implications for modern human origins". Am. J. Hum. Genet. 67:901-25. (2000) Online citation.

- Tishkoff SA, Ruano G, Kidd JR, Kidd KK. "Distribution and frequency of a polymorphic Alu insertion at the plasminogen activator locus in humans". Hum. Genet. 97:759-64. (1996) Online citation.

- Tsirka SE, Gualandris A, Amaral DG, Strickland S. "Excitotoxin-induced neuronal degeneration and seizure are mediated by tissue plasminogen activator". Nature 377:340-4. (1995) Online citation.

- Yang-Feng TL, Opdenakker G, Volckaert G, Francke U. "Human tissue-type plasminogen activator gene located near chromosomal breakpoint in myeloproliferative disorder". Am J Hum Genet 39:79-87. (1986) Online citation.

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© 2012 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan