Web document 8.2. Searching Rfam with a nucleotide query to find noncoding RNAs in genomic DNA.
GenBank accession U13369 (42,999 base pairs) includes ribosomal DNA matching 18S rRNA (accession NR_003286, 1,871 base pairs matching U13369 from nucleotides 3657 to 5527) and 5.8S rRNA (accession NR_003285, 156 base pairs matching from 6624-6779).
To search the Rfam database, which currently limits queries to 2 kilobases, use the following 201 nucleotides from clone U13369 encompassing 5.8S rRNA. An Rfam search page is at http://rfam.sanger.ac.uk/search.
>gb|U13369.1|HSU13369:6600-6800 Human ribosomal DNA complete repeating unit
GCCCTCGCCAAATCGACCTCGTACGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCTAGCTGCGAGAATTAATGTGAATTGCAGGACACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGCCGATCAATCGCCCCGGGGG