rs28080640 SNP Detail

Summary

• ID
  rs28080640
• Variation Type
  SNP
• Alleles
  A/T

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

Genome Location and Flanking Sequence

• Location
  Chr4:98435093 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                        TGGCAGATGT GACTCTTAGC TTGAGGGAGA GATTGAAATG
  AGCTTCAGTG ATTGTTTCCC ATGGTAGGAA CAGAATGGCA GGTTGCCCTT TAAAAGAATA
  W
  AATCGGAGGG AAAAAGAATA GAGGCCCAAG GTCGTGGGAA GAGAGGACAG AGTTGGAGAG
  AGTGGAGCTG CTTCCAGCAT CTTCCTGTCA GGAATGCAGC                      
  
  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	KK/HlJ	MOLF/EiJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss38243563	NES09530015	PERLEGEN	MM_PANEL2	f	SNP	A	A	A	A	A	A	A	A	A	T	A	A	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	KK/HlJ	MOLF/EiJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs28080640					SNP	A	A	A	A	A	A	A	A	A	T	A	A	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
ss38243563	NES09530015	PERLEGEN	MM_PANEL	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:98435093 () 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			1147 bp distal
Rr595753	regulatory region 595753			1271 bp distal
Rr595754	regulatory region 595754			within coordinates
Rr595755	regulatory region 595755			128 bp proximal
Tssr1238	transcription start site region 1238			232 bp downstream
Tssr37887	transcription start site region 37887			201 bp downstream
Tssr37888	transcription start site region 37888			167 bp downstream
Tssr37889	transcription start site region 37889			147 bp downstream
Tssr37890	transcription start site region 37890			117 bp downstream
Tssr37891	transcription start site region 37891			93 bp downstream
Tssr37892	transcription start site region 37892			51 bp downstream
Tssr37893	transcription start site region 37893			41 bp upstream
Tssr37894	transcription start site region 37894			63 bp upstream