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  EyeBrowse
  This site displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome.

The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes.

In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region.

To see the same region at the full UCSC site, cut and paste the location from the "position" window of the genome browser.

EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display.

Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.

Questions and feedback for EyeBrowse and EyeSAGE, UCSC browser tools, and EyeBrowse error messages are welcome.



  Human Genome Browser Gateway
 
The UCSC Genome Browser was created by the Genome Bioinformatics Group of UC Santa Cruz.
Software Copyright (c) The Regents of the University of California. All rights reserved.
clade genome assembly position or gene name image width  
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  About the Human Feb. 2009 (hg19) assembly (sequences)
 
human
Homo sapiens
(Graphic courtesy of CBSE)

The February 2009 human reference sequence (GRCh37) was produced by the Genome Reference Consortium.

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST or STS marker, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the human genome. See the User's Guide for more information.

Request:
   Genome Browser Response:

chr7 Displays all of chromosome 7
chrUn_gl000212 Displays all of the unplaced contig gl000212
chr3:1-1000000 Displays first million bases of chr 3, counting from p-arm telomere
chr3:1000000+2000 Displays a region of chr3 that spans 2000 bases, starting with position 1000000

RH18061;RH80175
Displays region between genome landmarks, such as the STS markers RH18061 and RH80175. This syntax may also be used for other range queries, such as between uniquely determined ESTs, mRNAs, refSeqs, etc.

D16S3046 Displays region around STS marker D16S3046 from the Genethon/Marshfield maps. Includes 100,000 bases on each side as well.
AA205474 Displays region of EST with GenBank accession AA205474 in BRCA1 cancer gene on chr 17
AC008101 Displays region of clone with GenBank accession AC008101
AF083811 Displays region of mRNA with GenBank accession number AF083811
PRNP Displays region of genome with HUGO Gene Nomenclature Committee identifier PRNP
NM_017414
Displays the region of genome with RefSeq identifier NM_017414
NP_059110
Displays the region of genome with protein accession number NP_059110

pseudogene mRNA Lists transcribed pseudogenes, but not cDNAs
homeobox caudal Lists mRNAs for caudal homeobox genes
zinc finger Lists many 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 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..


Assembly Details

The GRCh37 build reference sequence is considered to be "finished", a technical term indicating that the sequence is highly accurate (with fewer than one error per 10,000 bases) and highly contiguous (with the only remaining gaps corresponding to regions whose sequence cannot be reliably resolved with current technology). Future work on the reference sequence will focus on improving accuracy and reducing gaps in the sequence. Statistics for the GRCh37 build assembly can be found on the NCBI Build 37.1 Statistics web page.

Note on chrM
Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as "chrM" in the Genome Browser) has been replaced in GenBank with the record NC_012920. We have not replaced the original sequence, NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge Reference Sequence (rCRS) in the next human assembly release.

Chromosome naming scheme
In addition to the "regular" chromosomes, the hg19 browser contains nine haplotype chromosomes and 59 unplaced contigs. If an unplaced contig is localized to a chromosome, the contig name is appended to the regular chromosome name, as in chr1_gl000191_random. If the chromosome is unknown, the contig is represented with the name "chrUn" followed by the contig indentifier, as in chrUn_gl000211. Note that the chrUn contigs are no longer placed in a single, artificial chromosome as they have been in previous UCSC assemblies. See the sequences page for a complete list of hg19 chromosome names.

The nine haplotype chromosomes are:
nameaccessionUCSC chr name
HSCHR6_MHC_APD_CTG1GL000250.1chr6_apd_hap1
HSCHR6_MHC_COX_CTG1GL000251.1chr6_cox_hap2
HSCHR6_MHC_DBB_CTG1GL000252.1chr6_dbb_hap3
HSCHR6_MHC_MANN_CTG1GL000253.1chr6_mann_hap4
HSCHR6_MHC_MCF_CTG1GL000254.1chr6_mcf_hap5
HSCHR6_MHC_QBL_CTG1GL000255.1chr6_qbl_hap6
HSCHR6_MHC_SSTO_CTG1GL000256.1chr6_ssto_hap7
HSCHR4_1_CTG9GL000257.1chr4_ctg9_hap1
HSCHR17_1_CTG5GL000258.1chr17_ctg5_hap1

See the Wellcome Trust Sanger Institute MHC Haplotype Project web site for additional information on the chr6 alternate haplotype assemblies.

The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) that were taken from the corresponding regions in the X chromosome and are exact duplicates:

chrY:10001-2649520 and chrY:59034050-59363566
chrX:60001-2699520 and chrX:154931044-155260560

Bulk downloads of the data are available from the UCSC downloads server via ftp or http. We recommend that you use rsync or ftp for downloading large or multiple files.

The hg19 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.