Reference SNP(refSNP) Cluster Report: rs29559462

Reference SNP(refSNP) Cluster Report: rs29559462

refSNP ID: rs29559462
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:	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 ss39588881 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs29559462 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
ss39588881	ABI\|mCV22993277		fwd/T	A/G	acagcaaacacgtggcagctggtggcctgg	ggactcatctggctcaaattttcataattg	07/16/05	12/22/05	125	Genomic			unknown

Fasta sequence (Legend)

 ACTACGTAGT TCTAAGAAAG AATAAAACAA GGGGAGTTTT TCCAGAAGTT TCATGCTGAG
 GCTCATGTCG GCATACATAT ACACCCAGAT TGCTGGCTCC ACTGTTGTTA TAATACCGTG
 AGGCTCGGAG CCTCTGTGAG CAGGGTCCTG GTCCCCTTGG ATGTTGCCTG GCCAAGGAAC
 CTGGGAATTA TGAGCTGTCC AGGTCTAGCC TGGTACTGTC CTTTATTTCT CATGGTGAAT
 GACTAGATGG TGATGGCTGA GGAGTTCCTC ACAGCAAACA CGTGGCAGCT GGTGGCCTGG
 R
 GGACTCATCT GGCTCAAATT TTCATAATTG GACTCCTGAG CCTGAGACCT GTAGACAGGA
 GAAAATCAAC TTACCACCCA ATATGTGGCG AGGTCCTTGA CTTCCCAAGC TGTGCCCCAA
 CAACAGGTCA AGAAAGATAC TACATGGGAG GCAGTGGAGC CAGAAGCAGC AAGGCTGGGG
 AATTGATTAA CATAAGACAG GGGGATGGAT GCTGCTGGTG ATAGCGTCCT TGATCAGTTA
 CCATCTCCTA CAAAGTGACT TTGTCAGAGG TTTCAGACCC CAGCTCCATG TCCCCAATCT

GeneView

GeneView via analysis of contig annotation: Siglec15 sialic acid binding Ig-like lectin 15

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_001030635->XM_916291

function

C57BL/6J

NT_039676->XM_884636

function

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


Celera	NW_001030635->XM_916291->XP_921384	40551333	reverse	synonymous	C	Pro [P]	3	316
				contig reference	T	Pro [P]	3	316

C57BL/6J	NT_039676->XM_884636->XP_889729	110813	reverse	synonymous	C	Pro [P]	3	316
				contig reference	T	Pro [P]	3	316

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs29559462 maps exactly once on NCBI mouse chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NT_039676.7	110813	78240431	plus	A	ref_strain	C57BL/6J	C57BL/6J	view	300
18	NW_001030635.1	40551333	79184460	plus	A	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced

dbSNP Blast Analysis
GenBank HTGS Finished:
AC126553.4

Population Diversity

	Sample Ascertainment				Genotype Detail
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	G/G
ss39588881	CRAMUS_MOUSE		6	IG	2	1

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