D16S539

CODIS Core

D16S539 is a tetranucleotide short tandem repeat (STR) locus on chromosome 16 (16q24.1), one of the 20 CODIS core loci.

Basic Information

Chromosome

Cytogenetic Location

16q24.1

STRNaming template (FSSG)

GATA[n]

Type

Tetranucleotide

Alternative motifs (STRbase, historical notation)

[GATA]n rs11642858, [GATA]n rs114697632

Reference Allele

Explore internal sequence structure

See how the STRNaming name of the reference allele maps onto its sequence: repeat blocks, flanking regions and flanking variants.

Open STR Motif Explorer

See the reads at this locus

Open the built-in IGV viewer on the hg38 window of this marker with a 1000 Genomes sample.

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Genomic Coordinates

GRCh38/hg38

Repeat region

chr16:86,352,702-86,352,745 (44 bp)

GRCh37/hg19

Repeat region

chr16:86,386,308-86,386,351 (44 bp)

Motif and sequences are shown on the forward (+) strand of GRCh38.

Sequence structure (FSSG)

ISFG minimum range, bracketing and kit coverage from the Forensic Sequence Structure Guide, FSSG v6.1 (STRidER; distributed as FSSG_v6-1_beta.xlsx).

STRNaming Formatted ISFG Minimum Range for Common Alleles (FSSG)

GATA[n]

Reference allele (GRCh38) named with STRNaming 1.2.1

CE11_GATA[11]

Historical bracketing (2016-2023)

[GATA]11

ISFG minimum range (GRCh38)

chr16:86,352,698-86,352,749 (52 bp)

MPS kits covering this locus

PowerSeq 46GY (Does not cover the whole ISFG minimum range.)
ForenSeq Signature Prep/Plus and MainstAY
Precision ID GlobalFiler NGS STR Panel v2
IDSeek OmniSTR Global

Kit range does not cover the whole ISFG minimum range of this locus (chr16:86,352,698-86,352,749), according to the kit ranges in the FSSG. Bases of the minimum range outside a kit's range are not sequenced by that kit; bases filled in from the reference should be identified as such.

Allele frequencies at a glance

Most common allele per population group, with its frequency and the sample size, in the capillary electrophoresis data of pop.STR / SP-SMART.

Africa: Allele 12 (0.303, n = 503)
Native American: Allele 11 (0.271, n = 543)
East Asia: Allele 9 (0.275, n = 224)
Central and South Asia: Allele 11 (0.358, n = 194)
Europe: Allele 11 (0.291, n = 2,103)
Middle East: Allele 11 (0.326, n = 158)
Oceania: Allele 12 (0.280, n = 25)

Allele frequencies by population group (pop.STR, CE). Alleles absent from every group are omitted.
Allele	AFR	NAM	EAS	CSA	EUR	MES	OCE
5	0	0	0	0	0.001	0	0
8	0.046	0.030	0.002	0.028	0.018	0.013	0.020
9	0.137	0.186	0.275	0.144	0.154	0.142	0.020
10	0.088	0.108	0.129	0.116	0.098	0.066	0.140
11	0.284	0.271	0.232	0.358	0.291	0.326	0.240
12	0.303	0.237	0.259	0.229	0.266	0.259	0.280
13	0.109	0.144	0.076	0.121	0.147	0.180	0.220
14	0.030	0.022	0.027	0.003	0.024	0.009	0.080
15	0.002	0.003	0	0	0.001	0.003	0

Allele frequencies by population group (pop.STR, CE). Alleles absent from every group are omitted.

Variant Alleles

STRbase reports 50 sequence variants across 13 allele designations.

12.1

Related markers

Other CODIS core loci

Browse the full STR marker catalog