TPOX

CODIS Core

TPOX is a tetranucleotide short tandem repeat (STR) locus on chromosome 2 (2p25.3), one of the 20 CODIS core loci.

Basic Information

Chromosome

Cytogenetic Location

2p25.3

STRNaming template (FSSG)

TGAA[n]

Type

Tetranucleotide

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.

Open IGV Viewer

Genomic Coordinates

GRCh38/hg38

Repeat region

chr2:1,489,653-1,489,684 (32 bp)

GRCh37/hg19

Repeat region

chr2:1,493,425-1,493,456 (32 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)

TGAA[n]

Reference allele (GRCh38) named with STRNaming 1.2.1

CE8_TGAA[8]

Historical bracketing (2016-2023)

[AATG]8

ISFG minimum range (GRCh38)

chr2:1,489,647-1,489,692 (46 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 (chr2:1,489,647-1,489,692), 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

ForenSeq MainstAY/Signature Prep range shown is exclusive of primer, inferred bases may be included in UAS output. 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 8 (0.335, n = 505)
Native American: Allele 8 (0.409, n = 543)
East Asia: Allele 8 (0.496, n = 226)
Central and South Asia: Allele 8 (0.436, n = 194)
Europe: Allele 8 (0.558, n = 658)
Middle East: Allele 8 (0.500, n = 160)
Oceania: Allele 9 (0.380, 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
6	0.018	0.040	0	0.003	0.002	0.006	0
7	0.010	0.010	0	0	0.003	0.006	0
8	0.335	0.409	0.496	0.436	0.558	0.500	0.120
9	0.273	0.126	0.119	0.090	0.097	0.159	0.380
10	0.105	0.073	0.044	0.082	0.066	0.087	0.120
11	0.254	0.273	0.312	0.363	0.255	0.216	0.340
12	0.005	0.067	0.027	0.026	0.020	0.025	0.040
13	0	0.003	0.002	0	0	0	0

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

Variant Alleles

STRbase reports 20 sequence variants across 10 allele designations.

Related markers

Other STR markers on chromosome 2

Other CODIS core loci

Browse the full STR marker catalog