UCSC browser gives two sets of exons for a Refseq ID (f and r) - SNP interpretation?

Question

[warren.anderson]

In some cases, the UCSC table browser gives two sets of exons for a single Refseq ID (f and r). In the case for rattus Tnf (NM_012675), only the reverse strand entry shows up in ncbi (http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=248350).

For NM_012675, here is what the UCSC table browser gives (https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=461425005_930eITty7H8FQKJGaa5ILj87GaaY&boolshad.hgta_printCustomTrackHeaders=0&hgta_ctName=tb_refGene&hgta_ctDesc=table+browser+query+on+refGene&hgta_ctVis=pack&hgta_ctUrl=&fbUpBases=200&fbQual=exon&fbExonBases=0&fbIntronBases=0&fbDownBases=200&hgta_doGetBed=get+BED):

chr20	4855828	4856158	NM_012675_exon_0_0_chr20_4855829_f	0	+
chr20	4856657	4856712	NM_012675_exon_1_0_chr20_4856658_f	0	+
chr20	4856860	4856908	NM_012675_exon_2_0_chr20_4856861_f	0	+
chr20	4857193	4858446	NM_012675_exon_3_0_chr20_4857194_f	0	+
chr20	5189382	5190635	NM_012675_exon_0_0_chr20_5189383_r	0	-
chr20	5190920	5190968	NM_012675_exon_1_0_chr20_5190921_r	0	-
chr20	5191116	5191171	NM_012675_exon_2_0_chr20_5191117_r	0	-
chr20	5191670	5192000	NM_012675_exon_3_0_chr20_5191671_r	0	-

I am trying to match rat SNP coordinates to exon coordinates and I am having difficulty understanding what the proper annotation of SNPs should be. For example, SNPs in the + strand do not identify with Tnf in NCBI, as is the case for SNPs in the - strand, whereas the + and - coordinates are associated with Tnf in the UCSC browser. How should I interpret SNPs in exons of one strand versus the other?

Answer 1

[elvissober]

Try Ugene browser, that is the only thing what is good there, you know...

[andrew.j.skelton73]

Would I be wrong to think you work for UGene?

[Michael]

I have problems understanding the motivation, Ugene is free open source, so there is no big point in guerilla marketing it. The answer is incorrect and misleading for obvious reasons, and I would like to ultimately ask elvis on which evidence this recommendation is based. It can't be based on experience, because elvis admittedly has no experience with variant annotation tools.

In general it is a bad idea given a specific question is asked about one tools, to give the answer use another, or you better know what you are saying.