GGRNA | transcript search

Search tips:

GGRNA is a Google-like search engine for genes and transcripts archived in NCBI RefSeq.
RefSeq includes genomic, mRNA, noncoding RNA (ncRNA), and protein records.
Of these, GGRNA searches for RefSeq mRNA (accession starts with NM_/XM_) and ncRNA (NR_/XR_) records.
FTP: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/complete/complete.*.rna.gbff.gz
Search is always case insensitive.
Search for a phrase by enclosing it in double quotes (e.g. "PAZ domain").
By putting spaces before and after a keyword, you can avoid hitting longer words including the keyword within.
(e.g. " lamin " will avoid hitting flamingo)
GGRNA will find results that contain all the terms separated by spaces or commas.
Word order does not affect search results.
Any keyword which gives more than 10,000 hits will be ignored.
Advanced search is available for refining your query.
Instead, you can refine your query by using operators (see below: shown in green).

Search operators:

Search words	Description	Alias
refid:NM_001518	Search by RefSeq ID. Version number following a dot is ignored: [ refid:NM_003380.2 ] and [ refid:NM_003380 ] will return the same results. Words starting with NM_, XM_, NR_, or XR_ is automatically treated as refid: search without operator.	refseqid: refseq: id:NM_ id:XM_ id:NR_ id:XR_
geneid:10579	Search by Gene ID. An integer is automatically treated as geneid: search without operator.	gene:integer id:integer
symbol:VIM	Search for gene symbols and synonyms which partially match to the query. For example, query EIF2C will return EIF2C1, 2, 3, and 4.	name: gene:word
aa:KDEL	Search for amino acid sequence.
ref:Naito ref:1327585	Full text search within cited references. PubMed ID can also be queried.	reference:
probe:1552311_a_at probe:A_23_P101434	Search for nucleotide sequences by microarray probe ID. Words ending with _at, _st (Affymetrix ID) and starting with A_ (Agilent ID) are automatically treated as probe: search without operator. When probe ID is not converted into sequences, the probe ID is subjected to a basic search.	probeid:
anot:GO:0006915 anot:[chromatin] anot:"EC 2.3.1.51"	Search for annotation. - Search by Gene Ontology ID and term - Search by Enzyme Commission (EC) number	annotation: annot:
seq:caagaagagattg seq1:caagaagagattg seq2:caagaagagattgcc seq3:caaggagagatgggacac	Search for nucleotide sequence. Query containing letters A,T,G,C, and U only will automatically be treated as seq: search without the operator. U and T will be treated identically. seq1:, seq2:, and seq3: will return results with 1-, 2-, and 3-nucleotides mismatch tolerance.	sequence: sequence1: sequence2: sequence3:
comp:caagaagagattg comp1:caagaagagattg comp2:caagaagagattgcc comp3:caaggagagatgggacac	Search for complementary sequence. comp1:, comp2:, and comp3: will return results with 1-, 2-, and 3-nucleotides mismatch tolerance.	complementary: complementary1: complementary2: complementary3:
both:caagaagagattg both1:caagaagagattg both2:caagaagagattgcc both3:caaggagagatgggacac	Simultaneously retrieve sense and antisense nucleotide sequences corresponding to the query. both1:, both2:, and both3: will return results with 1-, 2-, and 3-nucleotides mismatch tolerance.	bothseq: bothseq1: bothseq2: bothseq3:
iub:aggtcannrtgacct iubcomp:aggtcannrtgacct iubboth:aggtcannrtgacct	Search for nucleotide sequence containing IUB code letters (i.e. N, R, Y, ...). iubcomp: will return complementary sequences to the query; iubboth: will return both strands.	iubseq: → iub:

GGRNA REST API:

GGRNA provides a simple REST API through a following URI:
http://GGRNA.dbcls.jp/api/species/query+string[.format]
- species → 'hs' for Homo sapiens, 'mm' for Mus musculus, etc.
- query+string → a simple keyword or a URI-encoded string.
- format → 'txt' or 'json' as output format. (optional)
Currently available species and format types are listed here:
- http://GGRNA.dbcls.jp/api/
Examples:
- http://GGRNA.dbcls.jp/api/hs/NM_001518.txt
  (Search "NM_001518" in human. Output in tab delimited text format.)
- http://GGRNA.dbcls.jp/api/mm/homeobox.txt
  (Search "homeobox" in mouse. Output in tab delimited text format.)
- http://GGRNA.dbcls.jp/api/dm/%22RNA+interference%22.json
  (Search "RNA interference" in D. melanogaster. Output in JSON format.
  Note that a double quote is encoded as %22, and a space character is encoded as + in the URI.)
- http://GGRNA.dbcls.jp/api/hs/caagaagagattg.json
  (Search "caagaagagattg" in human. Output in JSON format.)

What's new:

2013-07-26 Database updated to RefSeq rel. 60 (Jul, 2013).
2013-05-07 Database updated to RefSeq rel. 59 (May, 2013).
2013-03-15 Database updated to RefSeq rel. 58 (Mar, 2013).
2013-01-15 Database updated to RefSeq rel. 57 (Jan, 2013).
2012-11-14 Database updated to RefSeq rel. 56 (Nov, 2012).
2012-09-21 Database updated to RefSeq rel. 55 (Sep, 2012).
2012-07-18 Database updated to RefSeq rel. 54 (Jul, 2012).
2012-05-29 GGRNA paper has been published in Nucleic Acids Research.
2012-05-14 Database updated to RefSeq rel. 53 (May, 2012).
2012-03-09 Database updated to RefSeq rel. 52 (Mar, 2012).
2012-02-25 GGRNA REST API is available. See the help page.
2012-01-13 Database updated to RefSeq rel. 51 (Jan, 2012).
2011-11-17 Advanced search released.
2011-11-11 Database updated to RefSeq rel. 50 (Nov, 2011).
2011-09-20 Ciona intestinalis (sea squirt) is available.
2011-09-16 Search by Gene ontology and EC (Enzyme Commission) numbers enabled.
2011-09-16 Database updated to RefSeq rel. 49 (Sep, 2011).
2011-08-17 URL has been changed: http://GGRNA.dbcls.jp/en/
2011-07-29 Nucleotide sequence containing IUB code letters (e.g. N,R,Y,...) can be queried using iub: tag.
2011-07-27 X. tropicalis (frog) and O. sativa (rice) are available. Updated to RefSeq rel. 48 (Jul, 2011).
2011-07-04 English page launched.

Human	Mouse	Rat	Chicken
Frog	Zebrafish	Sea squirt	Fly
Worm	Arabidopsis	Rice
S. cerevisiae	S. pombe