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rs28080642 SNP Detail
Summary
  • ID
    rs28080642
  • Variation Type
    SNP
  • Alleles
    G/T
Genome Location and Flanking Sequence
  • Location
    Chr4:98434806 (GRCm39)
  • SNP Orientation to the Genome
    forward
  • SNP Reference Flanking Sequence
                                                TGATTTTGTG CTGGAAGCAA
    TAAGGAAGAG AAATGTTGGT GACTCTTCTG AACTGGGGGC AAGCTTAAAT CCATAGCTGC
    CTTTAATTTG CATGGGAAAG ATGCTGTCCC CCGAAGCACT GCCTCTCAGC AGGAAAATGG
    GACATTAACA TGTTATCAAT AGAAGCTGGC CACAAAATAA ATAGTTGTGT TTGTATTGCC
    K
    CCTGCTCTGA AATAGAGCTG TCTTTCCTGT GTGCACAGGG TGGCTGGTGT CACAGCCTGC
    AGCATGCAGT CCCTAAGTAT GCAGGGTGAC CGAGCGTCAG GGCCAGCAGC AGCCTGCAGC
    ATCCAAGGAT CTGACTGGAG AACCAGGGAT TTTTGCCGGC AGACCTTGCA GGCAGCTCTC
    ACCTACTGGC AGATGTGACT                                            
    
    K = G/T
    

    Note: Sequence in lower case indicates low-complexity or repetitive sequence
    BLAST SNP flanking sequence against the mouse Genome
SNP Assays
and
SNP Consensus
Strain alleles of submitted assays, and consensus values for this SNP
Legend
Assay ID Submitter
SNP ID
Submitter
Handle
Population
ss orientation
Variation Type
129S1/SvImJ
A/J
AKR/J
BALB/cByJ
BTBR T<+> Itpr3/J
C3H/HeJ
CAST/EiJ
DBA/2J
FVB/NJ
KK/HlJ
MOLF/EiJ
NOD/ShiLtJ
NZW/LacJ
PWD/PhJ
WSB/EiJ
ss38243565 NES09530012 PERLEGEN MM_PANEL2 f SNP G G G G G G T G G G T G G T G
SNP Consensus Information
SNP Consensus Type
129S1/SvImJ
A/J
AKR/J
BALB/cByJ
BTBR T<+> Itpr3/J
C3H/HeJ
CAST/EiJ
DBA/2J
FVB/NJ
KK/HlJ
MOLF/EiJ
NOD/ShiLtJ
NZW/LacJ
PWD/PhJ
WSB/EiJ
rs28080642 SNP G G G G G G T G G G T G G T G
Additional submitted assays for this SNP, where the strain of origin for observed alleles is not specified by the submitter
Assay ID Submitter
SNP ID
Submitter
Handle
Population
ss orientation
Variation
Type
Alleles
ss38243565 NES09530012 PERLEGEN MM_PANEL f SNP G/T
Gene/Marker
Associations
and
Function
Classes
MGI genes/markers associated with the SNP
Location: Chr4:98434806 () rs orientation: forward
Symbol Name Transcript Protein Function
Class
Allele Residue Codon
Position
AA
Position
Patj PATJ, crumbs cell polarity complex component Intron
Rr595752 regulatory region 595752 860 bp distal
Rr595753 regulatory region 595753 984 bp distal
Rr595754 regulatory region 595754 within coordinates
Rr595755 regulatory region 595755 415 bp proximal
Tssr1238 transcription start site region 1238 45 bp upstream
Tssr37887 transcription start site region 37887 62 bp upstream
Tssr37888 transcription start site region 37888 93 bp upstream
Tssr37889 transcription start site region 37889 127 bp upstream
Tssr37890 transcription start site region 37890 141 bp upstream
Tssr37891 transcription start site region 37891 177 bp upstream
Tssr37892 transcription start site region 37892 228 bp upstream
Tssr37893 transcription start site region 37893 328 bp upstream
Tssr37894 transcription start site region 37894 350 bp upstream

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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last database update
03/18/2025
MGI 6.24
The Jackson Laboratory