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

Polymorphism Information

NameALFRED UIDLocus NameLocus Symbol
TPA25 Alu insertionSI000152IPlasminogen activator, tissuePLAT
FstAvg Het# Populations Typed
0.0870.457191
Synonyms: rs4646972 ;
Frequency Display Formats:     
Estimated Heterozygosity: 
Frequency Download:   
External Resources:  Typing Protocol Record  GenBank sequence Record  GenBank sequence Record  dbSNP ss# Record  PharmGKB Variant Information Record  
References: See References
Polymorphism Description:  Alu element insertion polymorphism is located in intron 8 of gene PLAT, which spans sequence position 28463-29469 in GenBank K03021. By typing protocol giving, there are fragments of 260 bp and 570 bp for the Alu absent and present, respectively.
Ancestral Allele:  Alu Absent
Ancestral Allele Determine by: PCR of 38 non-human primates
Alleles:
Allele NameAllele SymbolDescription
Alu Deletion-ancestral chromosome, Alu element absent: 5'-ccctatgagatta "no 311 bp" gaacactacattac-3'
Alu Insertion+derived chromosome, Alu element present: 5'-ccctatgagatta "311 bp" gaacactacattac-3'

References:
- Antunez-de-Mayolo G, Antunez-de-Mayolo A, Antunez-de-Mayolo P, Papiha SS, Hammer M, Yunis JJ, Yunis EJ, Damodaran C, de Pancorbo MM, Caeiro JL, Puzyrev VP, Herrera RJ. "Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions". Electrophoresis 23:3346-3356. (2002)
Online citation.

- Batzer MA, Arcot SS, Phinney JW, Alegria-Hartman M, Kass DH, Milligan SM, Kimpton C, Gill P, Hochmeister M, Ioannou PA, Herrera RJ, Boudreau DA, Scheer WD, Keats BJB, Deininger PL, Stoneking M. "Genetic variation of recent Alu Insertions in human populations". J Mol Evol 42:22-29. (1996) Online citation.

- Chakrabarti CS, Roy M, Sengupta NK, Lalthantluanga R, Majumder PP. "Genetic relationships among some tribal groups inhabiting the north-eastern, eastern and sub-Himalayan regions of India". Ann Hum Genet 66:361-368. (2002) Online citation.

- Comas D, Calafell F, Benchemsi N, Helal A, Lefranc G, Stoneking M, Batzer MA, Bertranpetit J, Sajantila A. "Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits". Hum Genet 107:312-9. (2000) Online citation.

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

- Deininger PL, Sherry ST, Risch G, Donaldson C, Robichaux MB, Soodyall H, Jenkins T, Sheen F-m, Swergold G, Stoneking M, Batzer MA. "Interspersed repeat insertion polymorphisma for studies of human molecular anthropology. In Genomic diversity: Applications in human population genetics (ed. Papiha, Deka, and Chakraborty)". New York: Kluwer Academic/Plenum Publishers 201-212. (1999)

- Majumder PP, Roy B, Banerjee S, Chakraborty M, Dey B, Mukherjee N, Roy M, Thakurta PG, Sil SK. "Human-specific insertion/deletion polymorphisms in Indian populations and their possible evolutionary implications ". Eur J Hum Genet 7:435-46. (1999) Online citation.

- Nasidze I, Risch GM, Robichaux M, Sherry ST, Batzer MA, Stoneking M. "Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus". Eur J Hum Genet 9:267-72. (2001) Online citation.

- Novick GE, Novick CC, Yunis J, Yunis E, Antunez De Mayolo P, Scheer WD, Deininger PL, Stoneking M, York DS, Batzer MA, Herrera RJ. "Polymorphic Alu insertions and the Asian origin of Native American populations". Hum Biol 70:23-39. (1998) Online citation.

- Perna NT, Batzer MA, Deininger PL, Stoneking M. "Alu insertion polymorphism: A new type of marker for human population studies". Human Biology 64:641-648. (1992)

- Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, Jenkins T, Tahir MA, Deininger PL, Batzer MA. "Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa ". Genome Res 7:1061-71. (1997) 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.

- Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending HC, Rogers AR, Jorde LB. "Patterns of ancestral human diversity: An analysis of Alu-insertion and restriction-site polymorphisms". Am J Hum Genet 68:738-752. (2001) Online citation.

- Xiao FX, Yang JF, Cassiman JJ, Decorte R "Diversity at eight polymorphic Alu insertion loci in Chinese populations shows evidence for European admixture in an ethnic minority population from northwest China". Hum Biol 74:555-68. (2002) 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.

- de Pancorbo MM, Lopez-Martinez M, Martinez-Bouzas C, Castro A, Fernandez-Fernandez I, Antunez de Mayolo G, Antunez de Mayolo A, Antunez de Mayolo P, Rowold DJ, Herrera RJ. "The Basques according to polymorphic Alu insertions". Hum Genet 109:224-233. (2001) Online citation.


© 2017 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