Spidey Input

Before going on to alignments, it is a good idea to make an annotation file that documents the position of transcripts within your genomic fragment. In order to do this, map the Il1a and Il1b mRNAs onto the genomic fragment using the NCBI tool Spidey.

In the genomic sequence section, copy and paste the mouse genomic sequence that covers Il1a and Il1b into the text box or use the "browse" button to find the sequence file that you previously saved on your computer. In the mRNA input section, enter the accession number for the Il1a (X01450) mRNA sequence.

Choose Vertebrate under "Genomic sequence is:" and Summary only under "Output options:"; then hit align.

Genomic sequence (FASTA or GI/Accession):

Upload file:

>mouse_IL1a_IL1b
AGACAGTAAAAGAAAACAGGGGTAAAAGAATTAAAAACCAACTG
AAACATTCTCATGGTATACAATTGTGCTACCTGAATAAACTTAT
AAATTATTTAAAAGTGCTATGAAAAAAAAAGAGTGTGCATTTCT
TAAATTGGTCCATAAATTTCTCTACATCAGAGTCACTAACAAAA
TAACCTAACTTTACTAATAATCTACTTCTACAAATTCTTTCTAA

From: To:

mRNA sequence(s) (One or more FASTA or GI/Accession):

Upload file:

divergent sequences
Use large intron sizes

Minimum mRNA-genomic identity %
Minimum length of mRNA covered %

Genomic sequence is:

Vertebrate
Drosophila
C. elegans
Plant

Output options:

Text/summary
Summary only
ASN.1
Print multiple alignment

Nature Immunology 5, 768 – 774 (2004)