ALFRED detailed record information
|Name||ALFRED UID||Locus Name||Locus Symbol |
|MspI ||SI000167O||Homeo box B4||HOXB4|
Synonyms: rs3809782 ;
|Fst||Avg Het||# Populations Typed|
Frequency Display Formats:
External Resources: Genbank sequence Record Typing Protocol Record GenBank sequence Record dbSNP ss# Record PharmGKB Variant Information Record
References: See References
Polymorphism Description: A C/T SNP upstream of HOXB4 created by the disruption of the ancestral MspI recognition site, CCGG, to CTGG. The original Southern Blotting typing of this as an RFLP showed a rare third "allele" in the two pygmy populations, Biaka and Mbuti, that involved a second MspI site, the frequencies of which have been added to allele 2=C. With the PCR protocol provided, the site-absent allele gives a 560 bp fragment and the site-present allele gives 350 bp and 210 bp fragments following digestion with MspI.The alleles are coded as "1" (site absent) and "2" (site present).
Ancestral Allele: Site Present
Ancestral Allele Determine by: Digestion of PCR Product on primate (Chimp, Bonobo, Gorilla, Orangutan) DNA
|Allele Name||Allele Symbol||Description|
|MspI Site Absent||T||5'-cattaaatat C T GG ggccccat-3'|
|MspI Site Present||C||5'-cattaaatat C C GG ggccccat-3'|
- 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.
- Ogura T, Castiglione CM, Pakstis AJ, Kidd KK. "An MspI polymorphism for the HOX2F gene". Nucleic Acids Res. 19:1716. (1991) Online citation.
© 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