rs28080638 SNP Detail

Summary

• ID
  rs28080638
• Variation Type
  SNP
• Alleles
  A/T

• Created in dbSNP Build
  125
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr4:98435183 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCTCACCTAC TGGCAGATGT
  GACTCTTAGC TTGAGGGAGA GATTGAAATG AGCTTCAGTG ATTGTTTCCC ATGGTAGGAA
  CAGAATGGCA GGTTGCCCTT TAAAAGAATA AAATCGGAGG GAAAAAGAAT AGAGGCCCAA
  GGTCGTGGGA AGAGAGGACA GAGTTGGAGA GAGTGGAGCT GCTTCCAGCA TCTTCCTGTC
  W
  GGAATGCAGC AACCCTGAAG AGAGCAGTCC TGCAGCATGG TCCACGGGGG CTTCCCAGGT
  AAGGCTTCCG CTGCTGACGA GAGCTGCAGG TCTTGCTACA TGCAGTCAAA TGCTGCTTTA
  ATGTTGGTGC AGAGTAGCAT GCCGTTTAAT GATCTAAACA GGAGTAAGCT AAGGCATCTC
  TCTGAAGTGA GAGGGTAGGG                                            
  
  W = A/T
  

  
  Note: Sequence in lower case indicates low-complexity or repetitive sequence

  ---

SNP Assays
and
SNP Consensus

Strain alleles of submitted assays, and consensus values for this SNP

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
ss38243561	NES09530020	PERLEGEN	MM_PANEL2	f	SNP	A	A	A	A	A	A	A	A	A	A	A	A	A	T	A
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
rs28080638					SNP	A	A	A	A	A	A	A	A	A	A	A	A	A	T	A

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
ss38243561	NES09530020	PERLEGEN	MM_PANEL	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:98435183 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Patj	PATJ, crumbs cell polarity complex component			Intron
				mRNA-UTR
Rr595752	regulatory region 595752			1237 bp distal
Rr595753	regulatory region 595753			1361 bp distal
Rr595754	regulatory region 595754			within coordinates
Rr595755	regulatory region 595755			38 bp proximal
Tssr1238	transcription start site region 1238			322 bp downstream
Tssr37887	transcription start site region 37887			291 bp downstream
Tssr37888	transcription start site region 37888			257 bp downstream
Tssr37889	transcription start site region 37889			237 bp downstream
Tssr37890	transcription start site region 37890			207 bp downstream
Tssr37891	transcription start site region 37891			183 bp downstream
Tssr37892	transcription start site region 37892			141 bp downstream
Tssr37893	transcription start site region 37893			37 bp downstream
Tssr37894	transcription start site region 37894			within coordinates