Reference SNP(refSNP) Cluster Report: rs16798289

Reference SNP(refSNP) Cluster Report: rs16798289

refSNP ID: rs16798289
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	123/128
Map to Genome Build:	37.1

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Strain:	not submitted
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24752346 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16798289 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss24752346	ROCHEBIO\|Masp2_JC9287_3		fwd/T	A/G	tttgtcttctttagcntaaaaggctggttc	agtttatattcaaccttgagggctcaagtt	05/28/04	08/05/04	123	Genomic		A	unknown
ss37803069	PERLEGEN\|NES09112658		rev/B	C/T	aacttgagccctcaaggttgaatataaact	gaaccagccttttaagctaaagaagacaaa	04/27/05	07/28/05	125	Genomic			100 %

Fasta sequence (Legend)

 TTTACCTGCA AGTCATTGGA AAAGCAAAAA TGTTTAGCTG TAGTTGTCAT TTGCTTGAAT
 AACCCCTTGA AAAATGTTGA TTCTTGAGCA TCTGTGGTGG GGAGAGGTGT GTGAATAACC
 ATTTTACATG ATTTCATAAA TAGGTGTCTG CATTACCATG TTTGCTTGCA AAGTGGAAAC
 CTTTTAGATG TGTAACTTGA ATATGTATCA AGATCTCAAG TGCTTAATGA TAAGGTTTTG
 ACTTGTTAAA TTAAACCATT TGGAATATAT TGTGTGTTTG TAGTAGTCAT TTACTAGATA
 TGATCTGTTT TCAGATTCCT GCAAATTGAC ATTAAAGTCA CTTTNAACTG CAATATTTCA
 CTTAGCACAT GGGAGAAAGG CCTTTTAATC CTTTGTCTTC TTTAGCNTAA AAGGCTGGTT
 C
 R
 AGTTTATATT CAACCTTGAG GGCTCAAGTT CCAAATACCA CCCATCCCTC CATGAAGAAG
 GTACTTACCA TTGCTGCTCA TTGTNTAGAA AGTCTCTTCA CAGCTGTACT GAATCACAGC
 TTTGTAGGTA GTCACTTNAG GGCCTGTGAT ATAGTCCACA TGGCCATTGG GTA

GeneView

GeneView via analysis of contig annotation: Tardbp TAR DNA binding protein

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: Masp2 mannan-binding lectin serine peptidase 2

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

Celera

NW_001030773->NM_001003898

function

Celera

NW_001030773->NM_001003899

function

Celera

NW_001030773->NM_001008545

function

Celera

NW_001030773->NM_001008546

function

Celera

NW_001030773->NM_145556

function

C57BL/6J

NT_039268->NM_001003898

function

C57BL/6J

NT_039268->NM_001003899

function

C57BL/6J

NT_039268->NM_001008545

function

C57BL/6J

NT_039268->NM_001008546

function

C57BL/6J

NT_039268->NM_145556

function

Celera

NW_001030773->NM_001003893

function

C57BL/6J

NT_039268->NM_001003893

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


Celera	NW_001030773->NM_001003898->NP_001003898	852900	reverse	3' near gene

Celera	NW_001030773->NM_001003899->NP_001003899	852900	reverse	3' near gene

Celera	NW_001030773->NM_001008545->NP_001008545	852900	reverse	3' near gene

Celera	NW_001030773->NM_001008546->NP_001008546	852900	reverse	3' near gene

Celera	NW_001030773->NM_145556->NP_663531	852900	reverse	3' near gene

C57BL/6J	NT_039268->NM_001003898->NP_001003898	2446466	reverse	3' near gene

C57BL/6J	NT_039268->NM_001003899->NP_001003899	2446466	reverse	3' near gene

C57BL/6J	NT_039268->NM_001008545->NP_001008545	2446466	reverse	3' near gene

C57BL/6J	NT_039268->NM_001008546->NP_001008546	2446466	reverse	3' near gene

C57BL/6J	NT_039268->NM_145556->NP_663531	2446466	reverse	3' near gene

Celera	NW_001030773->NM_001003893->NP_001003893	852900	forward	intron

C57BL/6J	NT_039268->NM_001003893->NP_001003893	2446466	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs16798289 maps exactly once on NCBI mouse chromosome 4

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
4	NT_039289.1	99341	unplaced	minus	T	alt_strain_1	129/SvEvTac	129/SvEvTac	view	421
4	NT_039268.5	2446466	147986344	minus	T	ref_strain	C57BL/6J	C57BL/6J	view	421
4	NW_001030773.1	852900	150873515	minus	T	alt_assembly_1	Celera	Celera	view	421

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
RPAMMSEQ0037245	NC_000070.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank STS:
AL591032.19 AL606969.26 CU207387.6	BV164194.1

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	G/G
ss24752346	RPAMM		42	IG	20	1

ss37803069	MM_PANEL2		30	IG	14	1

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.091+/-0.193	31	31	5	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .