Description
This description is taken from:
National Institute of Standards and Technology
Brief Introduction to STRs.
Tandemly repeated DNA sequences are widespread throughout the human genome
and show sufficient variability among individuals in a population that they
have become important in several fields including genetic mapping, linkage
analysis, and human identity testing. These tandemly repeated regions of DNA
are typically classified into several groups depending on the size of the
repeat region. Minisatellites (variable number of tandem repeats, VNTRs) have
core repeats with 9-80 bp, while microsatellites (short tandem repeats, STRs)
contain 2-5 bp repeats. The forensic DNA community has moved primarily towards
tetranucleotide repeats, which may be amplified using the polymerase chain
reaction (PCR) with greater fidelity than dinucleotide repeats. The variety of
alleles present in a population is such that a high degree of discrimination
among individuals in the population may be obtained when multiple STR loci
are examined.
The region definitions are obtained from:
National Institute of Standards and Technology
FBI CODIS Core STR Loci
gene genomic location repeating sequences (STRs)
locus
TPOX chr2:1,489,568-1,489,738 AATG
D3S1358 chr3:45,540,612-45,540,935 TCTA/TCTG
FGA chr4:154,587,511-154,588,005 TTTC/TTTT/TTCT/CTTT/CTCC/TTCC
D5S818 chr5:123,775,262-123,775,937 AGAT
CSF1PO chr5:150,076,172-150,076,490 AGAT
D7S820 chr7:84,159,945-84,160,482 GATA
D8S1179 chr8:124,894,738-124,895,197 TCTA/TCTG
TH01 chr11:2,170,711-2,171,770 AATG/ATG
VWA chr12:5,983,825-5,984,174 TCTA/TCTG/TCCA
D13S317 chr13:82,147,846-82,148,218 TATC/AATC
D16S539 chr16:86,352,320-86,352,912 GATA
D18S51 chr18:63,281,248-63,282,317 AGAA
D21S11 chr21:19,181,866-19,182,275 TCTA/TCTG
AMELX chrX:11,296,605-11,296,939 polymorphism
AMELY chrY:6,869,982-6,870,187 polymorphism
01 Jan 2017 added:
D1S1656 chr1:230,769,329-230,769,904 TAGA/TAGG
D2S441 chr2:68,011,777-68,012,172 TCTA
D2S1338 chr2:218,014,601-218,015,031 TGCC/TTCC
D10S1248 chr10:129,294,018-129,294,623 GGAA
D12S391 chr12:12,296,826-12,297,399 AGAT/AGAC
D19S433 chr19:29,925,974-29,926,466 AAGG/AAAG/TAGG
D22S1045 chr22:37,140,171-37,140,616 ATT/ACT
Display
All of these regions can be seen in one genome browser session using the
'multi-region' function to display them together as a set:
genome.ucsc.edu/s/Hiram/hg38.codis.
The display indicates the regions of the genome amplified by the PCR primers,
the aligment of the PCR primers to the genome, and the repeating pattern of
the STR elements selected by the primers.
Credits
This display was constructed by
Hiram Clawson at the
U.C. Santa Cruz Genomics Institute.
References
National Institute of Standards and Technology
FBI CODIS Core STR Loci
National Institute of Standards and Technology
Overview of STR Fact Sheets
with references to all publications for each of the STR systems.
Erin Butler, Richard Li: CUNY John Jay College
Genetic Markers for Sex Identification in Forensic DNA Analysis 21 Aug 2014.
Shadrach B, Commane M, Hren C, Warshawsky I.
A rare mutation in the primer binding region of the
amelogenin gene can interfere with gender identification.
J Mol Diagn. 2004 Nov;6(4):401-5. doi: 10.1016/S1525-1578(10)60538-7.
PMID: 15507681; PMCID: PMC1876427.
Grubwieser P, Mühlmann R, Parson W.
New Sensitive Amplification Primers for the STR Locus D2S1338 for Degraded Casework DNA
Int J Legal Med 2003 Jun;117(3):185-8. doi: 10.1007/s00414-002-0359-y.
Epub 2003 Feb 11.
Natsuko Mizuno, D.V.M.; Tetsushi Kitayama, M.Sc.; Koji Fujii, Ph.D.;
Hiroaki Nakahara, D.V.M.;Kanako Yoshida, Ph.D.; Kazumasa Sekiguchi, Ph.D.;
Naoto Yonezawa, Ph.D.; Minoru Nakano, Ph.D.; and Kentaro Kasai, Ph.D.
A D19S433 Primer Binding Site Mutation and the Frequency in
Japanese of the Silent Allele It Causes
J. Forensic Sci,September 2008, Vol. 53, No. 5 doi: 10.1111/j.1556-4029.2008.00806.x
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