Fetching Transcription Start And End For A Custom Gene List From Ucsc (Hg18/Ncbi36)

Question

[asingal]

I want transcription start and end for the gene (hg18/NCBI36). I used UCSC it does not have all the genes i am interested in. Your help will be appreciated.

Thanks!

[Neilfws]

Might want to read that title again. Hint: transpiration is how plants move water.

[Sukhi Singh]

Excuse me :)))

[asingal]

i just have list of gene symbols

[Sukhi Singh]

Sounds really funny, which genes you have are not there. If you could post the geneNames, fetching would be really easy.

Answer 1

[Sukhi Singh]

I dont think, that you are pointing to gene name, they might be identifiers. Anyways, make a text file for your genes, one per line.

• Go to TableBrowser and select

  clade-> Mammal,

  genome-> Human,

  group-> Gene and Gene prediction Tracks,

  track->RefSeq Genes,

  table->refgene

• Click on paste list button in the line of identifiers (names/accessions):
• Copy paste the id's from the file you made earlier, if big, then use upload list, from the previous button.
• In the output format: select selected fields from primary and related table, click on get output and then select bin,name,chrom,strand,txStart,txEnd,name2
• Click on get output, copy-paste and save.

This essentially will contain all the co-ordinates of your genes of interest, column 5,6 are txStart and txEnd.

Cheers

Answer 2

[asingal]

Thank you very much for your help !!

Answer 3

[asingal]

After uploading the GB_ACC list i am getting a message saying:

•Note: 6153 of the 25847 given identifiers (e.g. AF520801) have no match in table refGene, field name or in alias table refLink, field name. Try the "describe table schema" button for more information about the table and field.

How should i describe table schema.

Thanks!