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GenAP

Querying the Genome Browser

You may browse to the default genome position of an assembly when clicking the "submit" button or you may specify a genome position in a variety of formats.

Valid position queries can include:

To specify a genome position:

  1. Select the desired clade, genome and assembly
  2. Enter the desired query in the "search term" box (see sample queries below)
  3. Click the "submit" button

Note: A query may have multiple results. If this is the case, a results page will appear listing each result along with the track it is associated with. Once selected, the result will be displayed in the Browser with a highlighted tag, making it easier to identify.

Sample queries

Below is a list of examples that might be used to query the Genome Browser. Note that not every query listed here will produce a result in every assembly. The list serves only to illustrate the different types of queries that can be performed.

QueryGenome Browser Response
chr7 Displays all of chromosome 7
chr3:1-1000000 Displays the first million bases of chromosome 3, counting from the p-arm telomere
chr3:1000000+2000 Displays a region of chromosome 3 that spans 2000 bases, starting with position 1000000
chrUn_gl000212 Displays all of the unplaced contig gl000212
chr6_GL285171_random Displays the unlocalized contig GL285171
GL192360 Displays all of scaffold GL192360
20p13 Displays the region for band p13 on chromosome 20
374180 Displays the region containing Entrez Gene identifier 374180
AA205474 Displays the region containing the EST with GenBank accession AA205474 in the BRCA1 cancer gene on chromosome 17
AC008101 Displays the region containing the clone with GenBank accession AC008101
AF083811 Displays the region containing the mRNA with GenBank accession number AF083811
NM_017414 Displays the region containing RefSeq identifier NM_017414
NP_059110 Displays the region containing protein accession number NP_059110
PRNP Displays the region containing HUGO Gene Nomenclature Committee identifier PRNP
RH18061;RH80175
15q11;15q13
rs1042522;rs1800370
Displays the region between genome landmarks, such as the STS markers RH18061 and RH80175, or chromosome
bands 15q11 to 15q13, or SNPs rs1042522 and rs1800370. This syntax may also be used for other range queries,
such as between uniquely determined ESTs, mRNAs, refSeqs, etc.
NM_000310.3(PPT1):c.271_287del17insTT
NM_007262.4(PARK7):c.-24+75_-24+92dup
NM_006172.3(NPPA):c.456_*1delAA
MYH11:c.503-14_503-12del
NM_198576.3(AGRN):c.1057C>T
NM_198056.2:c.1654G>T
NP_002993.1:p.Asp92Glu
NP_002993.1:p.D92E
BRCA1 Ala744Cys
LRG_100t1:c.4G>A
LRG_100t1:n.1
chrX:g.31500000_31600000del
NR_111987:n.-1
NM_015102.4:n.3086-2
NM_033517:c.1307_1309del
Displays the region containing HGVS term
pseudogene mRNA Lists transcribed pseudogenes, but not cDNAs
p53 Lists mRNAs related to the p53 tumor suppressor
T-cell receptor Lists mRNAs for T-cell receptor genes in GenBank
breast cancer Lists mRNAs associated with breast cancer
homeobox caudal Lists mRNAs for caudal homeobox genes
zinc finger Lists zinc finger mRNAs
kruppel zinc finger Lists only kruppel-like zinc fingers
huntington Lists candidate genes associated with Huntington's disease
zahler Lists mRNAs deposited by a scientist named Zahler
Evans,J.E. Lists mRNAs deposited by co-author J.E. Evans

Use this last format for author queries. Although GenBank requires the search format Evans JE, internally it uses the format Evans,J.E..