Zebrafish covert ids
BioMart is a very handy tool when you want to convert IDs from different databases. The following is a list of 31 IDs of zebrafish transcripts from the NCBI RefSeq database (http://www.ncbi.nlm.nih.gov/projects/RefSeq/): NM_001007404 NM_131505 NM_001109712 NM_001002203 NM_194399 NM_130952 NM_001083861 NM_001001832 NM_001005973 NM_131510 NM_001039980 NM_001020497 NM_001024214 NM_001114738 NM_001077553 NM_194404 NM_20112 NM_131359 NM_001020643 NM_001079958 NM_001161453 NM_001098737 NM_001077146 NM_131877 NM_152884 NM_001098619 NM_001020607 NM_001145592 NM_131128 NM_200720 NM_001020607
Generate a list that shows to which Ensembl Gene IDs and to which gene names these RefSeq IDs correspond. Do these 31 transcripts correspond to 31 genes?
Click New. Choose the Ensembl Genes database. Choose the Zebrafish genes dataset.
Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Select Input external references ID list - RefSeq mRNA ID(s) and enter the list of IDs in the text box (either comma separated or as a list). HINT: You may have to scroll down the menu to see these.
Count shows 37 genes (remember the zebrafish genome has haplotypes, which means many genes are duplicated).
Click on Attributes in the left panel. Select the Features attributes page. Select Gene name and Gene stable ID under GENE. Expand the EXTERNAL section by clicking on the + box. Select RefSeq mRNA ID from the External References section.
Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.
