CSF1PO

CODIS Core

CSF1PO is a tetranucleotide short tandem repeat (STR) locus on chromosome 5 (5q32), one of the 20 CODIS core loci.

Basic Information

Chromosome

Cytogenetic Location

5q32

STRNaming template (FSSG)

TCTA[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

chr5:150,076,324-150,076,375 (52 bp)

GRCh37/hg19

Repeat region

chr5:149,455,887-149,455,938 (52 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)

TCTA[n]

Reference allele (GRCh38) named with STRNaming 1.2.1

CE13_TCTA[13]

Historical bracketing (2016-2023)

[ATCT]13

ISFG minimum range (GRCh38)

chr5:150,076,318-150,076,380 (63 bp)

MPS kits covering this locus

PowerSeq 46GY
ForenSeq Signature Prep/Plus and MainstAY
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 (chr5:150,076,318-150,076,380), 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 12 (0.339, n = 505)
Native American: Allele 12 (0.314, n = 542)
East Asia: Allele 12 (0.404, n = 225)
Central and South Asia: Allele 12 (0.348, n = 194)
Europe: Allele 11 (0.321, n = 655)
Middle East: Allele 12 (0.341, n = 160)
Oceania: Allele 12 (0.447, n = 19)

Allele frequencies by population group (pop.STR, CE). Alleles absent from every group are omitted.
Allele	AFR	NAM	EAS	CSA	EUR	MES	OCE
6	0.002	0	0	0	0.002	0	0
7	0.018	0.038	0.011	0	0.005	0.003	0
8	0.050	0.032	0	0	0.004	0.009	0.053
9	0.081	0.037	0.040	0.010	0.019	0.006	0.026
10	0.274	0.239	0.229	0.276	0.276	0.284	0.263
11	0.196	0.280	0.233	0.322	0.321	0.297	0.105
12	0.339	0.314	0.404	0.348	0.305	0.341	0.447
13	0.036	0.052	0.069	0.041	0.050	0.053	0.105
14	0.004	0.009	0.013	0.003	0.017	0.006	0
15	0	0	0	0	0.002	0	0

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

Variant Alleles

STRbase reports 27 sequence variants across 11 allele designations.

10.3

Related markers

Other STR markers on chromosome 5

Other CODIS core loci

Browse the full STR marker catalog