Reference SNP(refSNP) Cluster Report: rs33352225

Reference SNP(refSNP) Cluster Report: rs33352225

refSNP ID: rs33352225
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	125/128
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 ss39524919 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs33352225 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
ss39524919	ABI\|mCV24297661		fwd/B	C/T	tctttgatggctacgactgtgaaatccctc	aacctgcatgtgagcctgggaatgaggggc	07/16/05	12/22/05	125	Genomic			unknown
ss56334984	ENSEMBL\|NT_039649.5_11115256		fwd/B	C/T	tctttgatggctacgactgtgaaatccctc	aacctgcatgtgagcctgggaatgaggggc	06/11/06	06/11/06	127	Genomic			unknown

Fasta sequence (Legend)

 CCCCTGGGTT GGGCAACCCG GGCTTTCAAT GCACCTGCCC TCCTGACTCT CCAGGGCCCC
 GGTGTCAAAG GCCAGGGGCA AGTGGGTGTG AGGGCCGAGG TGGTGATGGG ACCTGCGATG
 CTGGCTGCAG TGGCCCAGGA GGAGACTGGG ATGGAGGGGA CTGTTCCCTG GGGGTCCCAG
 ACCCCTGGAA GGGCTGTCCC CCGCATTCCC AGTGCTGGCT TCTGTTCCGG GACGGACGGT
 GTCACCCGCA GTGTGACTCT GAGGAGTGTC TCTTTGATGG CTACGACTGT GAAATCCCTC
 Y
 AACCTGCATG TGAGCCTGGG AATGAGGGGC AGGGGTGGGG GTGGGAGACA TACATGCCCA
 AGCTGCAGAA TGACCAGCAT TGGACGCCAA GGAGTTTCCA TGCTAAAAAA GACTCTAGGT
 TCCAACCCAG TGGAATGGAG TGACAGACAC TGTGGGACAT GGGCCTCAGC TTCTCTCCCC
 ACTTTTACCA TAGAATGCCT CCCTGGAAAA CAACACCCCC CCCCCCCCCC GCCGCCCAAG
 GGAAAGGGTC TTGGATCCTC TTTCTGAGAC AGGAGCAGGA GGAAAGGTTG GCCCCAGTCA

GeneView

GeneView via analysis of contig annotation: Notch4 Notch gene homolog 4 (Drosophila)

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_001030616->NM_010929

function

C57BL/6J

NT_039649->NM_010929

function

129/SvJ

NT_039662->NM_010929

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


Celera	NW_001030616->NM_010929->NP_035059	100107	forward	missense	C	Pro [P]	2	1245
				contig reference	T	Leu [L]	2	1245

C57BL/6J	NT_039649->NM_010929->NP_035059	20913644	forward	missense	C	Pro [P]	2	1245
				contig reference	T	Leu [L]	2	1245

129/SvJ	NT_039662->NM_010929->NP_035059	831682	forward	missense	C	Pro [P]	2	1245
				contig reference	T	Leu [L]	2	1245

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs33352225 maps exactly once on NCBI mouse chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NT_039649.7	20913644	34719858	plus	T	ref_strain	C57BL/6J	C57BL/6J	view	300
17	NT_039662.2	831682	34719873	plus	T	alt_strain_16	129/SvJ	129/SvJ	view	300
17	NW_001030616.1	100107	37678075	plus	T	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_039649.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC006289.1 CT009767.6	AC091703.6 CU457785.6

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	T/T
ss39524919	CRAMUS_MOUSE		8	IG	2	2

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	-1.000+/-0	4	4	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 .