D2S1338

CODIS Core

D2S1338 is a tetranucleotide short tandem repeat (STR) locus on chromosome 2 (2q35), one of the 20 CODIS core loci.

Basic Information

Chromosome

Cytogenetic Location

2q35

STRNaming template (FSSG)

GGAA[n]GGCA[n]

Type

Tetranucleotide

Alternative motifs (STRbase, historical notation)

[GGAA]n [GGCA]n, [GGAA]2 GGAC [GGAA]n [GGCA]n, [GGAA]n GAAA [GGAA]2 [GGCA]7, [GGAA]n GGGA [GGCA]7

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

chr2:218,014,859-218,014,950 (92 bp)

GRCh37/hg19

Repeat region

chr2:218,879,582-218,879,673 (92 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)

GGAA[n]GGCA[n]

GGAA[2]GGAC[1]GGAA[n]GGCA[n]

GGAA[n]GAAA[1]GGAA[2]GGCA[7]

GGAA[n]GGGA[1]GGCA[7]

Reference allele (GRCh38) named with STRNaming 1.2.1

CE23_GGAA[2]GGAC[1]GGAA[13]GGCA[7]

Historical bracketing (2016-2023)

[GGAA]2 GGAC [GGAA]13 [GGCA]7

ISFG minimum range (GRCh38)

chr2:218,014,855-218,014,954 (100 bp)

MPS kits covering this locus

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

Kit range does not cover the whole ISFG minimum range of this locus (chr2:218,014,855-218,014,954), 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.

Notes from the FSSG

Originally characterized on the reverse strand

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 19 (0.247, n = 505)
Native American: Allele 19 (0.172, n = 542)
East Asia: Allele 19 (0.202, n = 225)
Central and South Asia: Allele 19 (0.162, n = 194)
Europe: Allele 17 (0.174, n = 2,105)
Middle East: Allele 17 (0.266, n = 160)
Oceania: Allele 19 (0.440, 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
13	0	0.001	0	0	0	0	0
14	0.029	0	0	0	0	0	0
15	0	0.003	0	0	0.001	0	0
16	0.039	0.054	0.004	0.008	0.043	0.063	0
17	0.112	0.171	0.093	0.085	0.174	0.266	0.060
18	0.075	0.061	0.109	0.111	0.076	0.097	0.040
19	0.247	0.172	0.202	0.162	0.140	0.087	0.440
20	0.145	0.093	0.131	0.162	0.134	0.191	0.100
21	0.058	0.077	0.029	0.028	0.051	0.019	0.100
22	0.137	0.085	0.042	0.077	0.063	0.056	0.040
23	0.062	0.118	0.162	0.160	0.111	0.100	0.140
24	0.060	0.080	0.158	0.121	0.096	0.072	0.080
25	0.029	0.063	0.062	0.072	0.086	0.050	0
26	0.008	0.018	0.007	0.013	0.022	0	0
27	0	0.004	0	0	0.003	0	0

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

Variant Alleles

STRbase reports 111 sequence variants across 15 allele designations.

Related markers

Other STR markers on chromosome 2

Other CODIS core loci

Browse the full STR marker catalog