Reference SNP(refSNP) Cluster Report: rs8251020

Reference SNP(refSNP) Cluster Report: rs8251020

refSNP ID: rs8251020
Organism:	mouse (Mus musculus)
Molecule Type:	Genomic
Created/Updated in build:	118/128
Map to Genome Build:	37.1

Allele
Variation Class:	DIP: deletion/insertion polymorphism
RefSNP Alleles:	-/A
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 ss12746571 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs8251020 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
ss12746571	ROCHEBIO\|AF133093_BS1736_11		fwd/B	-/A	gagtggtgggcagcaaggtcaagnngggna	tggcacacttcagaaacaaagctcactatg	10/17/03	04/07/04	118	Genomic		-	unknown

Fasta sequence (Legend)

 CATGAGATGT AAACTCTGAC CAAAACAAAA AACAGCAGGG TAgccagatg tggtggtgaa
 tacttttaat cccagcactt ggaagacaga cnggtggatc tctgaattca aggctagcct
 ggtccacaaa gtgagttgta gtatagcctg aactcatact cagagaaacc ctgtctcaaa
 agacaaaGCA AAGTANGTAA NTCTTGTAAG AAAGCAGAGA ATCGAGATGA AGGTNCNGAG
 TGGGTNNTGA GGAAGAATGT GAGTGGTGGG CAGCAAGGTC AAGNNGGGNA
 N
 TGGCACACTT CAGAAACAAA GCTCACTATG TANTAAATGA AGGAATCTAG CTGTTCAGCA
 GGAGGGACTG ATAGGGTACC CAACATAAGG TAGGAGCACT TCTAGTTGAT AGGAA

GeneView

GeneView via analysis of contig annotation: Abcd1 ATP-binding cassette, sub-family D (ALD), member 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_001035173->NM_007435

function

C57BL/6J

NT_039706->NM_007435

function

129/SvEvTac

NT_039745->NM_007435

function

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


Celera	NW_001035173->NM_007435->NP_031461	572220	forward	intron

C57BL/6J	NT_039706->NM_007435->NP_031461	18554055	forward	intron

129/SvEvTac	NT_039745->NM_007435->NP_031461	343901	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs8251020 maps exactly once on NCBI mouse chromosome X

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
X	NW_001035173.1	572220	64978307	plus	A	alt_assembly_1	Celera	Celera	view	290
X	NT_039706.7	18554055	70969948	plus	A	ref_strain	C57BL/6J	C57BL/6J	view	290
X	NT_039745.3	343901..343901	70970082..70970082	plus	A	alt_strain_1	129/SvEvTac	129/SvEvTac	view	287..290

NCBI Resource Links

Submitter-Referenced
dbSTS
RPAMMSEQ0000935

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank STS:
AC091453.2 AF133093.2 AL805924.5	AC023305.4 AC073154.9	BV089039.1 BV156186.1

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	-/-	A/A
ss12746571	RPAMM		20	IG	9	1

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.180+/-0.240	10	10	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 .