Dear Researchers,
1- I am working on RNA seq, and now I have transcriptome data and I have the different genes of interest from different resources, but I am looking for their full-length CDs from some I have found on (https://www.arabidopsis.org) and some have not found. so how can find?
2-I have different Genes such as CER12, BCF1, CER10-39, and would like to find their full-length CDs, as I have searched on NCBI (all database, genes, nucleotides), but some have given a list of items related to CER12, so which one should I select and on which basis?
3- if I have not found the given any information such as the gene ID or gene information such as for BCF1 so how can find the CDs?
Follow this link
https://plants.ensembl.org/biomart/martview
Than select Ensembl Plants gene and slect any model species for instance Arabidopsis Thaliana
wait for it to load the DB
One it is loaded, select Filter option from left panel, than click on + sign in Gene
A very long list of options will open, now click on check box " Input external references ID list", then from drop down menu select Gene Name(s) [e.g. ZPR4], than paste your list of genes in given box.
Once you pasted your list, then click on attribute from left side panel and then select sequence option, click on + sign SEQUENCES: , and select whatever kind of sequence is appropriate for you. there are plenty of option including
"Unspliced (Transcript)
Unspliced (Gene)
Flank (Transcript)
Flank (Gene)
Flank-coding region (Transcript)
Flank-coding region (Gene)
5' UTR
3' UTR
Exon sequences
cDNA sequences
Coding sequence
Peptide"
Once you are done with selection, click on "Count" tab at top left corner, wait for it to complete the fetching calculation once you see some numeric values, click on "results" tab. Save your output in desired format.
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