Reference SNP(refSNP) Cluster Report: rs16821690

Reference SNP(refSNP) Cluster Report: rs16821690

refSNP ID: rs16821690
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:	C/T
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 ss24777426 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16821690 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
ss24777426	ROCHEBIO\|Pttg1_JC10507_7		fwd/B	C/T	agtgctaggattaaaggcatgtgccaccac	gccnggccttgtnaggcattcaccagattg	05/28/04	08/05/04	123	Genomic		T	unknown

Fasta sequence (Legend)

 ATGTATGTTG TATTAAAAAA GCATTTGTGC ATATGTTCAG ATNNTGAATA CTTAACCNAC
 CCCTGATTGG TATTTTTTGG TGTTAGGAGA CGCCACTGTT CTCCTTTGGA AGTAGACCCC
 TCAATGTGTC CCTTTTTGTG GCTGTTAGCT AGTGACAGTT ATTAGATCTC TTANTTAAGG
 AGTCACTCCC AGCTCATTTA GTATTTGTTA GGCATTCTTt ttttgttttt ttttgttttt
 gtttttgttt tttttttttt gagatagggt ttctctgtat agccctngct gtcctggaac
 tcactttgta gancaggctg gccttgaact caaatccacc tgcctntgcc tcccaagtgc
 taggattaaa ggcatgtgcc accac
 Y
 gccnggcCTT GTNAGGCATT CACCAGATTG GTTTAGTTCT AATGACTTTA GTATTCAGTA
 ACNAGAATTG AAAGGCTCTG AGTCTTTGAG AACNGTC

GeneView

GeneView via analysis of contig annotation: Pttg1 pituitary tumor-transforming 1

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_001030461->NM_013917

function

C57BL/6J

NT_096135->NM_013917

function

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


Celera	NW_001030461->NM_013917->NP_038945	505410	reverse	3' near gene

C57BL/6J	NT_096135->NM_013917->NP_038945	8738297	reverse	3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs16821690 maps exactly once on NCBI mouse chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NT_096135.5	8738297	43233419	minus	A	ref_strain	C57BL/6J	C57BL/6J	view	385
11	NW_001030461.1	505410	48048422	minus	A	alt_assembly_1	Celera	Celera	view	385

NCBI Resource Links

Submitter-Referenced
dbSTS
RPAMMSEQ0038999

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank STS:
AL670472.7	BV161468.1

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	T/T
ss24777426	RPAMM		6	IG	1	2

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.444+/-0.157	3	3	0	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 .