Track Descriptions & Citations

Tracks Built into this Server

Ensembl Gene Structure
Source: UCSC genome browser.
This track displays details about exon structures of Ensembl genes.

MGC Gene Structure
Source: UCSC genome browser.
This track gives information about exon structure of MGC genes.

Reference Gene Structure
Source: UCSC genome browser.
This track gives the information about exon structure of the reference genes

RefSeq Gene
Source: UCSC genome browser.
The RefSeq Genes track shows known protein-coding genes taken from the NCBI mRNA reference sequences collection (RefSeq). RefSeq mRNAs were aligned against the zebrafish genome using blat; those with an alignment of less than 15% were discarded. When a single mRNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were considered.

Other mRNAs
Source: UCSC genome browser.
This track displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank from organisms other than zebrafish. This track follows the display conventions for PSL alignment tracks. The methodology as follows; the mRNAs were aligned against the zebrafish genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were considered.

Ensembl Gene
Source: UCSC genome browser.
This track displays gene predictions which were generated by Ensembl. For the description of the methods used in Ensembl gene prediction, refer to Hubbard, T. et al. (2002).

VEGA Gene
Source: UCSC genome browser.
This track shows gene annotations from the Vertebrate Genome Annotation (Vega) database. The following information is excerpted from the Vertebrate Genome Annotation.
“The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analyzed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidences”. The Vega annotation consists of BAC and PAC clones that were sequenced for the zebrafish clone mapping and sequencing project. This is based on the tiling path information from the FPC database.

CONTRAST Gene Predictions
Source: CONTRAST database.
This track gives information about protein-coding gene predictions generated by CONTRAST database. The following information is excerpted from CONTRAST database. CONditionally TRAined Search for Transcript is a gene-prediction algorithm that uses sophisticated machine-learning techniques, has pushed de novo prediction accuracy to new heights, and has significantly closed the gap between de novo and evidence-based methods for human genome annotation.

GEN ID v1.3
Source: GEN ID
This track displays set of predictions using gene id program to predict genes along DNA sequence in zebrafish. The following information is excerpted from ‘gene id’ home page “its accuracy compares favorably to that of other existing tools, GEN ID is more efficient in terms of speed and memory usage and it offers some rudimentary support to integrate predictions from multiple source”.

ZGC gene
Source: UCSC genome browser.
This track shows alignments of Zebrafish mRNAs from the Zebrafish Gene Collection (ZGC) having full-length open reading frames (ORFs) to the genome. The GenBank Zebrafish ZGC mRNAs identified as having full-length ORFs were aligned against the genome using blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 1% of the best and at least 95% base identity with the genomic sequence were considered.

Transcripts with Affymetrix Probesets
Source: UCSC genome browser.
This track shows the location of both the consensus sequences and target sequences used for the selection of probes on the Affymetrix Zebrafish genome chip. This information is taken from UCSC Genome browser.

Transcripts with Wild Type Array Probesets
Source: UCSC genome browser.
This track shows expression data from the Zon Lab at Children's Hospital Boston using the Affymetrix Zebrafish Gene Chip Genome Array. Data is displayed in two sub tracks showing the alignments of either the probe set consensus sequences or target sequences for the Affymetrix Zebrafish Gene Chip. For detailed information about the experimental methods refer Weber et al. (2005).This expression data is for five strains of wild type Zebrafish whole embryos at different developmental stages.

Quadfinder G-Quadruplex Motifs
This track shows information regarding identification and analysis of Quadruplex-forming Motifs using Quadfinder tool.Ihe information is collected from IGIB.

miRBase v10 microRNAs
Source: miRBase database.
This track gives information about published danio rerio microRNA sequences and associated annotations from miRBase. The database contains over 5000 sequences from 58 species.

NXsensor
Source: NXsensor
This track gives information about DNA sequences that are likely to be nucleosome-free using a web based tool called NXSensor. The following information is excerpted from NXsensor homepage “It is a web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors”.

Morpholino
Source: ZFIN database
This track displays Morpholinos and their target sequences from zfin database.

ZF MODELS- Tilling data
Source: ZFMODELS database.
This track gives details about TILLING mutations mapped to zebrafish (zv7) genome.

Genes mutated by ENU
Source: ZFIN
This track gives the details about ENU mutants with their affected genes and genotypes

Sridhar Lab Transposon Insertions
(Patowary A and Sridhar S, Unpublished Results)
This track gives information about Tol2 transposon mediated gene traps in Zebrafish, from Dr Sridhar Sivasubbu lab.

ZNOMICS Retrovirus Insertions
Source: ZNOMICS
This track gives the information about retrovirus mediated insertion sequences which are curated from Znomics. The following information is excerpted from the Znomisc home page,” It delivers an innovative approach to whole animal compound screening program.

[x] Becker Lab Transposon Insertions
No additional information available.

[x] Ekker Lab Transposon Insertions
No additional information available.

[x] Hopkins Lab Retrovirus Insertions
No additional information available.

[x] Kawakami lab Transposon insertions
No additional information available.

[x] Korzh Lab Transposon Insertions
No additional information available.

[x] Parinov lab Transposon insertions
No additional information available.

[x] Johnson Lab Transposon Insertions
No additional information available.

Pesudogene predictions
Source: Pseudogenes database.
This track contains set of identified pseudo genes in zebrafish from pseudogenes.org database.

VEGA Pseudogene
Source: UCSC genome browser.
This track shows pseudogene annotations from the Vertebrate Genome Annotation (Vega) database. The following information is excerpted from vega homepage, “The Vega database is designed to be a central repository for high-quality, frequently updated manual annotation of different vertebrate finished genome sequence. Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analyzed on a clone-by-clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). The annotation is based on supporting evidence”.

Human Ortholog genes in Zebrafish - Predicted by Inparanoid
Source: Inparanoid database.
This track gives information about ZEBRAFISH and HUMAN gene orthologs from Inparanoid database, which is a comprehensive Eukaryotic Ortholog Database and has a collection of pairwise ortholog groups between 17 whole genomes.

Human Ortholog Genes in Zebrafish - Predicted by Homologene
Source: Homologene database.
This track gives the information about automated detection of homologs among the annotated genes between zebrafish and human.

ESTs
Source: UCSC genome browser.
This track shows alignments between Zebrafish expressed sequence tags (ESTs) in GenBank and the genome. ESTs are single-read sequences, typically about 500 bases in length that usually represent fragments of transcribed genes. This track was generated using following methodology; Zebrafish ESTs from GenBank were aligned against the genome using blat. When a single EST aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence are displayed in this track. This information is taken from UCSC.

ZFMODELS Carp EST
Source: ZFMODELS
This track displays Common carp (Cyprinus carpio) EST sequences mapped to the Zebrafish genome. Information collected from ZF-MODELS database.

DNA/GC Content
The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas.

Fugu chain
Source: UCSC genome browser.
This track shows alignments of Fugu (fr2, Oct. 2004) to the zebrafish genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both Fugu and zebrafish simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

Fugu Net
Source: UCSC genome browser.
This track shows the best Fugu/zebrafish chain for every part of the zebrafish genome. It is useful for finding orthologs regions and for studying genome rearrangement. The Fugu sequence used in this annotation is from the Oct. 2004 (fr2) assembly. Chains were derived from blastz alignments and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher-chains and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Tetraodon Net
Source: UCSC browser.
This track shows alignments of Tetraodon (tetNig1, Feb. 2004) to the Zebrafish genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both Tetraodon and zebrafish simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. Chains were derived from blastz alignments and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Tetraodon chain
Source: UCSC genome browser.
This track shows alignments of Tetraodon (tetNig1, Feb. 2004) to the Zebrafish genome using a gap scoring system.

Mouse Net
Source: UCSC genome browser.
This track shows the best mouse/zebrafish chain for every part of the zebrafish genome. It is useful for finding ortholog regions and for studying genome rearrangement. The mouse sequence used in this annotation is from the July 2007 (mm9) assembly. Chains were derived from blastz alignments, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Human chain
Source: UCSC genome browser.
This track shows alignments of human (hg18, Mar. 2006) to the Zebrafish genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and zebrafish simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

Human Net
Source: UCSC genome browser.
This track shows the best human/zebrafish chain for every part of the Zebrafish genome. It is useful for finding orthologs regions and for studying genome rearrangement. The human sequence used in this annotation is from the Mar. 2006 (hg18) assembly human sequence used in this annotation is from the Mar. 2006 (hg18) assembly. Chains were derived from blastz alignments and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher-level and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Medaka chain
Source: UCSC genome browser.
This track shows alignments of medaka (oryLat1, Apr. 2006) to the zebrafish genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both medaka and zebrafish simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species This track shows alignments of medaka (oryLat1, Apr. 2006) to the zebrafish genome using a gap scoring system.

Medaka Net
Source: UCSC genome browser.
This track shows the best medaka/zebrafish chain for every part of the zebrafish genome. It is useful for finding orthologs regions and for studying genome rearrangement. The medaka sequence used in this annotation is from the Apr. 2006 (oryLat1) assembly. Chains were derived from blastz alignments and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher-level and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Mouse chain
Source: UCSC genome browser.
This track shows alignments of mouse (mm9, July 2007) to the zebrafish genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both mouse and zebrafish simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

Assembly
Source: UCSC genome browser.
This track shows the Zebrafish Zv7 (July 2007) assembly provided by 'Welcome Trust Sanger Institute'. It contains scaffolds (supercontigs) totaling 1,440,582,308 bp. The assembly has been tied to the fingerprint contig (FPC) map (data freeze April 11, 2007), which provides a tiling path of sequenced clones. 1.02 Gb of sequence from 7,823 sequenced clones (7,139 finished and 684 unfinished) were used as a scaffold for the assembly. Gaps were filled with contigs from a whole genome shotgun (WGS) assembly of 5.5x coverage comprised of reads from a library created from a single Tuebingen doubled haploid zebrafish. Approximately 1.28 Gbp (89%) of the resulting integrated assembly were placed on chromosomes 1-25, including estimated gap sizes and 100 bp gaps inserted between scaffolds. The complete sequence of the mitochondrion genome, which is shown as chrM in the Genome Browser, was obtained from GenBank. The entire assembly of 5,036 scaffolds includes the 26 chromosomes and 5,010 unplaced scaffolds that fall into two groups.
1) Zv7_NAXX - WGS contigs that could not be related to any FPC contig and could not be placed on a chromosome (4,844 unmapped scaffolds)
2) Zv7_scaffoldXXXX - sequences based on FPC contigs or linked to chromosomes via a marker (166 unmapped scaffolds). The unplaced scaffolds contain 100 bp gaps that are shown in the Gap annotation. For more information about the assembly, see the Assembly annotation track description and the WTSI Danio rerio Sequencing Project website.

Contigs
Source: UCSC genome browser.
This track shows the location of the contigs of the July 2007 zebrafish Zv7 assembly from The Wellcome Trust Sanger Institute. A fingerprinted contigs (FPC) map was produced by restriction enzyme digestion with HindIII. Clones were selected from this for high-quality sequencing. To create the Zv7 assembly, a scaffold was produced using 1.02 Gb of sequence from 7,823 sequenced clones (7,139 finished and 684 unfinished). Whole genome shotgun (WGS) assembly contigs were added to fill in the gaps. The Zv7 assembly has a total sequence length of 1,440,582,308 bp consisting of 5,036 pieces: chromosomes 1-25, the complete mitochondrion genome (chrM obtained from GenBank), and 5,010 unplaced scaffolds. The WGS assembly consists of 131,933 contigs having an N50 length of 20,127 bp and 22,961 scaffolds (supercontigs) with an N50 length of 1,499,123 bp (n = 277). Of these, a total of 5,010 scaffolds are not mapped to chromosomes: 166 are in Zv7_scaffoldXXXX scaffolds (sequences tied to unplaced FPC contigs) and 4,844 are contained in Zv7_NAXX scaffolds (WGS contigs not tied to an FPC contig, chromosome unknown). For more information about the assembly, see the Assembly annotation track description and the WTSI Danio rerio Sequencing Project website.

Gap
Source UCSC Genome Browser
This track depicts gaps in the zebrafish assembly.This assembly contains the following principal types of gaps Fragment - gaps between the Whole Genome Shotgun contigs of a supercontig. (In this context, a contig is a set of overlapping sequence reads.) A supercontig is a set of contigs ordered and oriented during the Whole Genome Shotgun process using paired-end reads.) These are represented by varying 100 Ns in the assembly. Fragment gap sizes are usually taken from read pair data and Contig - gaps between supercontigs not linked by the fingerprint map, but instead by marker data. (In this context, the "Contig" gap type refers to a map contig, not a sequence contig.) In general, these are represented by 100 Ns in the assembly for all chromosomes Gaps of other sizes were used when mRNA or other data suggested possible but not confirmed links between supercontigs.

Simple Repeats
Source: UCSC genome browser.
This track displays simple tandem repeats (possibly imperfect) located by Tandem Repeats Finder (TRF) program, which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases. For more information refer-Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15; 27(2):573-80.

dbSNP
Source: ensembl
This track gives the information about dbSNP of 128 version mapping from ensembl. The db SNP determines the genomic locations of SNPs by aligning their flanking sequences to the zebrafish genome.

Interrupted Repeats
Source: UCSC genome browser.
This track shows joined fragments of interrupted repeats extracted from the output of the RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences using the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. (2000).

RepeatMasker
Source: UCSC genome browser.
This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence, as well as a modified version of the query sequence in which all the annotated repeats have been masked. RepeatMasker uses the RepBase library of repeats from the Genetic Information Research Institute (GIRI). RepBase is described in Jurka, J. (2000).

tRNAscan SE Predictions
Source: tRNAscan SE web server
This track gives information about predicted transfer RNA genes in Zebrafish genome, using tscanSE tools. tRNAscan -SE identifies 99-100% of transfer RNA genes in DNA sequences while giving less than1 false positive per 15 gigabases.For more information about the tscan SE refer-Lowe, T.M. and Eddy, S.R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 25, 955-964.

ANCORA Highly Conserved Noncoding Elements (HCNEs)
Source: ANCORA database.
This track gives information about highly conserved noncoding elements in Zebrafish from ANCORA database. ANCORA includes a genome browser that shows highly conserved noncoding elements locations and their novel features.

ECRbaseECR
Source : ECRbase
This track gives the details from ECRbase database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.This information is collected from Evolutionary Conserved Region Database.

miRBase microRNA Targets
Source: miRBase database.
This track displays information about miRNA targets in zebrafish genome, developed by Enright Lab at the Wellcome Trust Sanger Institute, containing predicted targets for danio rerio-microRNAs. The information is collected from miRBase database-A microRNA database.


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FishMap development has been generously funded by the Council for Scientific and Industrial Research (CSIR), India (Grant No FAC002)

FishMap is hosted and maintained at the G N Ramachandran Knowledge Center for Genome Informatics at the Institute of Genomics and Integrative Biology

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