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BUILD 129
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Reference SNP(refSNP) Cluster Report: rs1260409          
refSNP ID: rs1260409
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:87/129
Map to Genome Build:36.3
Allele
Variation Class:SNP:
single nucleotide polymorphism
RefSNP Alleles:A/G
Ancestral Allele:A
Clinical Association:unknown
HGVS Names
NM_004698.1:c.1035+424A>G
NT_004487.18:g.798491A>G
Links

SNP Details are organized in the following sections:
Submission Fasta Resource GeneView Map Diversity Validation

  Submitter records for this RefSNP Cluster back to top
The submission ss1932753 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1260409 during BLAST analysis for the current build.

NCBI
Assay ID		Handle|Submitter IDValidation
Status		ss to rs
Orientation
/Strand		Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date		Update
Date		Build
Added		Molecule
Type		Freq
Warning		Ancestral
Allele		Success
Rate
ss1932753KWOK|OVLP-000925-716920fwd/TA/Gttgtatttttggtggagacggggtttctcctgttggtcaggctggtctcgaactcctgac10/06/0010/10/0387Genomic99 %
ss3491036SC_JCM|AL365403.14_102460fwd/TA/Gttgtatttttggtggagacggggtttctcctgttggtcaggctggtctcgaactcctgac09/24/0110/10/03117Genomicunknown
ss16446258CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_032962.5_798491fwd/TA/Gttgtatttttggtggagacggggtttctcctgttggtcaggctggtctcgaactcctgac02/17/0403/04/04120Genomicunknown
ss20460231SSAHASNP|WGSA-200403-chr1.chr1.NT_032962.5_798491fwd/TA/Gttgtatttttggtggagacggggtttctcctgttggtcaggctggtctcgaactcctgac03/18/0403/18/04121Genomicunknown
ss41255145ABI|hCV2719800fwd/TA/Gttgtatttttggtggagacggggtttctcctgttggtcaggctggtctcgaactcctgac07/16/0507/17/05126Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1260409|allelePos=515|totalLen=1803|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=130
 CTCCATTGCC CCTTCCCAGC GCCAGAGACG CACTTTTAAA TTCCATGACA AGGGCAAATT
 TGAGAAGATT GCTCAGCGAT TACGGACAAA GGTATCTGGC TTAGAGTATA ACACAGAATT
 TGGAAAAAGT TAAGAAGCTG ACAAGAAAAC ATTGTTAAAT CTCTGTGTTC TAGGAAATTA
 GATAAATAGG TCATTTAAAG cagcagtcct caaccttttt ggcaccaggg acttgtttca
 tggaagataa tttttcccct ggagtaagga tggtttcgtg atggttcaag cacatagcat
 ttattgtgta ctttattatt attatttttt tcgagatgga gtgtcgctct tgttgcccag
 gctggagtgc aatggggcga tctcggcttg ctgcaacctt tgcctcccag gttcaagtga
 ttctcctgcc tcagcctccc gagtagctgg gatcacaggc atgtgccacc acgcctggct
 aattttgtat ttttggtgga gacggggttt ctcc
 R
 tgttggtcag gctggtctcg aactcctgac ctcaggtgat ctgcccactt tgtcctccca
 aagtgctggg attacaggcg tgagccaccg cccccgCCtt tttttttttt ttgggcgggg
 agggggatgg agtcttgcac tgttacctgg gctggagtgc agtggtacag tctcagctca
 ctgcaacctc tgcctcctgg gttcaagcaa ttctcctgcc tcagcctcct gagtagctgg
 gactgcaggc atgcgccgcc atgcctgacg aattttttgt atttttagta gagacagggt
 ttcactatgt tggcccggct ggtcttaaac tcctgacctt gtgatctgcc tgccttgacc
 tcccaaagtg ctgggattat aggcgtgagc cactgtgctg gcctatttct attattattt
 tattgtaata tatgatgaaa taattatata actcaccata atataaaatc actgggagcc
 ttgagcttgt tttcctgctg aaatggtccc atttgggtgt gatgggagac agtgacagat
 catcaggcat tagattctca taaggaatgt gcaacatagc cccctcacat gtacagttca
 caatagggtt cgcgctccta tgagaatctc atgccaccga tgatctgaca ggaggtggag
 ctcaggccat aatgcaggta atagggagca atcgtaagta cagatgagac tgttggcttg
 cctgctgctc acctcctgtt gtgcagccca gttcctaaaa gacTGTTGGG TTGGGGACCC
 CTGATTTAAA GCAATGAATA CTTTGAAAAA TGTgctggac aagatggctc aagcctgtaa
 tcccagcgct ttgggaggcc gaggtgggtg gatcacgagg tcaggagttc aagaccagcc
 tgcccaacat ggtgaaaccc cgtctctact aaaagtacaa aaattaaccg agcgtggtgg
 tgggtgcctg taatcctagc tacttgggag gctgagtcag gagaatcact tgaaactgga
 aggcagaggt tgcagtgagc tgagatcgca ccactgcact ccagcatggg caaaagagcg
 aaactccgtc tcaaaaaata tatatatata tttattaata taatacataa tttttttaGC
 AGATTTTACT TCCTAATTCG TTTCTACATA AGTGGAAATA TTATGAAATT GAGTTTGAAA
 ATTCTCCACA TACAACTAAG TGGAGGGAAA CAATTTGAAA CATTCTGAGT GACTAAGGAA
 GGCTTGCCTG TAGTTAAAAT TTAATGAG

  GeneView back to top
GeneView via analysis of contig annotation: PRPF3 PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)
View variations for gene:
Include clinically associated: in gene region cSNP has frequency double hit
Group
Label		Contig->mRNAGene Model (contig mRNA transcript) Color Legend
referenceNT_004487->NM_004698
function
HuRefNW_001838529->NM_004698
function
CeleraNW_925683->NM_004698
function
"
Group
label		Contig-->mRNA-->ProteinContig
position		mRNA
orientation		mRNA
pos		FunctiondbSNP
allele		Protein
residue		Codon
pos		Amino acid
pos
referenceNT_004487->NM_004698->NP_004689798491forwardintron
HuRefNW_001838529->NM_004698->NP_004689504669forwardintron
CeleraNW_925683->NM_004698->NP_004689460710forwardintron

GeneView: no link established by BLAST analysis of mRNA sequences
  Integrated Maps: back to top
NCBI MapViewer:  rs1260409 maps exactly once on NCBI human chromosome 1
ChromosomeContig
accession		Contig
position		Chromosome
position		Hit
orientation		Contig
Allele		Assembly
Type		Group
label		Contig
label		Neighbor
SNP		SNP_flank
position
1NW_001838529.1504669121686838plusGalt_assembly_8HuRefHuRefview514
1NW_925683.1460710123423884plusAalt_assembly_1CeleraCeleraview514
1NT_004487.18798491148574760plusAref_assemblyreferencereferenceview514

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_032962 AL359875 AL359883 AL365403.9
dbSNP Blast Analysis
GenBank HTGS Finished:GenBank HTGS Draft:
AL611942.12 AL359875.3 AL359883.7 AL365403.14

  Population Diversity back to top
There is no frequency data.

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation		PCR results confirmed
in multiple reactions		Homozygotes detected
in individual genotype data
byClusterwith2hit
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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Revised: May 25, 2006 1:38 PM .