Track Descriptions & Citations

Tracks Built into this Server

Ensembl Exons
Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Source:http://www.ensembl.org/index.html

RefSeq
The track lists the RefSeq Ids downloaded from Ensembl and mapped to ZV8. Source:http://www.ensembl.org/Danio_rerio/

Ensembl Transcripts
Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Source:http://www.ensembl.org/index.html

Ensembl Genes
Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Source:http://www.ensembl.org/index.html

GC content
Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Source:http://www.ensembl.org/index.html

SNP
The SNP data listed in this track was downloaded from Ensembl (BioMart) and was mapped to the chromosome positions available in BioMart.

Quadruplex
The track lists the Quadruplex-forming nucleotide sequences e in the ZV8 genome which are designed using the Quadfinder algorithm. Source:http://miracle.igib.res.in/quadfinder/

Histone 3'UTR stem-loop structure (HSL3)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Iron Responsive Element (IRE)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Selenocysteine Insertion Sequence (SECIS) - type 1
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs.Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Selenocysteine Insertion Sequence (SECIS) - type 2
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Cytoplasmic polyadenylation element (CPE)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

TGE translational regulation element (TGE)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

AU-rich class-2 Element (ARE2)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Internal Ribosome Entry Site (IRES)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR. These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Male specific lethal 3' UTR cis-acting element (MSL2-3UTR)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Bruno 3' UTR responsive element (BRE)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR . These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Androgen receptor GU-rich element (AR_CURE)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR. These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Upstream Open Reading Frame (uORF)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3 ' UTR. These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Gamma interferon activated inhibitor of Ceruloplasmin mRNA translation (GAIT element)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR. These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs.
$name is a $type spanning $ref from $start to $end. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

Mos polyadenylation response element (Mos-PRE)
The track lists the Regulatory Motifs in mRNA in 5' UTR and 3' UTR. These motifs are identified by an integrated web server RegRNA which can identify both sequence or structural homologs of regulatory RNA motifs. Source:http://regrna.mbc.nctu.edu.tw/php/browse.php?ShowType=1

miRNA
microRNAs are short RNA sequences which regulate the expression of the target genes. MiRNA sequences were downloaded from the online repository miRBASE and were mapped to the ZV8 genome using local BLAT. Source:http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Antagomirzyme
AntagomiRzymes are short DNAzyme sequences which are used to silence miRNAs. The AntagomiRzymes cleave at a particular purine-pyrimidine base pair This track lists all the possible AntagomiRzymes against all ZV8 miRNAs predicted by algorithms developed in-house. Source: http://www.ncbi.nlm.nih.gov/sites/entrez/19229913

Inparanoid
The Inparanoid eukaryotic ortholog database is a collection of pairwise comparisons between 35 whole genomes including Danio rerio. The Inparanoid program was developed at the Center for Genomics and Bioinformatics to address the need to identify orthologs.The InParanoid program uses the pairwise similarity scores, calculated using NCBI-Blast, between two complete proteomes for constructing orthology groups. Source:http://inparanoid.sbc.su.se/cgi-bin/index.cgi

GtRNAdb:tRNAscan-SE
The track lists Tranfer RNAs (tRNAs) which represent one of the class of non-protein coding RNA genes found in all living organisms. Genomic tRNA Database (GtRNAdb) is a web resource providing overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. The program tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence. Source:http:http://lowelab.ucsc.edu/GtRNAdb/Dreri/Dreri-summary.html

NXSENSOR
The track lists regions of DNA sequences that are likely to be nucleosome-free identified by in-house algorithm developed on the basis of the tool Nucleosome eXclusion Sensor (NXSensor). Source:http://www.sfu.ca/~ibajic/NXSensor/

TargetScan Targets
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. This track lists all possible miRNA target prediction using TargetScan, which searches for miRNA-target complementarity. This search is limited to six nucleotides of the seed region (bases 2-7). Source:http://www.targetscan.org/

RNAhybrid Targets
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. This track lists all possible miRNA target predictions using RNAHybrid which emphasises more on target structure rather than seed complementarity. The program finds regions in the 3’ UTR that have potential to form duplexes with miRNAs and produces information on the putative target site quality, the quantity of sites available, their conservation and the significance of the conservation. Source: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

miRanda Targets
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. miRanda is an algorithm for finding genomic targets for microRNAs. This track lists all possible miRNA target predictions using miRanda which searches for complementarity between miRNAs and 3' UTRs and calculates the thermodynamics of the binding sites. Source: http://www.microrna.org/microrna/home.do

Cellular Component
This track lists the Gene Ontology (GO) Ids that describe gene products in terms of their associated biological processes, cellular components and molecular functions. This data is fetched using BioMart. BioMart can directly access the data in Ensembl and is used to export tables of gene ontology. Source=http://www.ensembl.org/biomart/martview/

Molecular Function
This track lists the Gene Ontology (GO) Ids that describe gene products in terms of their associated biological processes, cellular components and molecular functions. This data is fetched using BioMart. BioMart can directly access the data in Ensembl and is used to export tables of gene ontology. Source=http://www.ensembl.org/biomart/martview/

Biological Process
This track lists the Gene Ontology (GO) Ids that describe gene products in terms of their associated biological processes, cellular components and molecular functions. This data is fetched using BioMart. BioMart can directly access the data in Ensembl and is used to export tables of gene ontology. Source=http://www.ensembl.org/biomart/martview/

KEGG Pathways
This track lists pathway information on Zebrafish. The information is obtained from KEGG PATHWAY which is a collection of manually drawn pathway maps representing the molecular interaction and reaction networks. Along with Pathway name the track also lists Pathway ID and the KEGG gene IDs involved in these pathways. Source:ftp://ftp.genome.jp/pub/kegg/genes/organisms/dre/dre_pathway.list

PDB IDs
This track lists the PDB IDs, represented by a 4 character identifier, for Zebrafish genes. This information is obtained from KEGG. These IDs may be used to retrieve information for the corresponding structure. Source:ftp://ftp.genome.jp/pub/kegg/genes/organisms/dre/dre_pdb.list

Pfam IDs
This track lists Pfam IDs along with KEGG identifiers for Zebrafish genes. The pfam IDs may be used to search for one or more functional regions, commonly termed domains. Different combinations of domains may give rise to the diverse range of proteins and thus, identification of domains that occur within proteins can provide insights into their function. Source:ftp://ftp.genome.jp/pub/kegg/genes/organisms/dre/dre_pfam.list

PROSITE IDs
This track lists Prosite IDs. PROSITE is a database of protein families and domains. Proteins or protein domains belonging to a particular family generally share functional attributes and these may be used to assign function to yet uncharacterized proteins based on the protein signatures. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. Source:ftp://ftp.genome.jp/pub/kegg/genes/organisms/dre/dre_prosite.list

Digital Gene Expression Tags
The track lists the GATC motifs identified by in-house algorithms..
$name is a $type spanning $ref from $start to $end. Source:http://tubic.tju.edu.cn/deg/

Erpin miRNA Predictions
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Other Predictions from Erpin
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Small Nucleolar RNA Predictions from Erpin
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Iron Response Element
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Histone 3' UTR stem-loop
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Nanos 3' UTR translation control element
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Bicoid 3'-UTR regulatory element
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

TrkB IRES
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Prion pseudoknot
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Voltage-gated potassium-channel Kv1.4 IRES
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

UnaL2 line 3
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR 11
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Ma3 gene ribosomal frameshift signal
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

GRIK4 3 prime UTR element
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

U5 spliceosomal RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

CsrB/RsmB RNA family
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Eukaryotic type signal recognition particle RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

U4 spliceosomal RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Vault RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

U2 spliceosomal RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

U1 spliceosomal RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Type I tRNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Type II tRNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

SRP RNA Domain IV
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Eukaryotic 5S rRNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

RtT RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

FGF-1 internal ribosome entry site (IRES)
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Antizyme RNA frameshifting stimulation element
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

L-myc internal ribosome entry site (IRES)
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

ctRNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

U6atac minor spliceosomal RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Potassium channel RNA editing signal
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Pseudoknot of the domain G(G12) of 23S ribosomal RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Arthropod 7SK RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Invasion gene-associated RNA
Erpin is a RNA motif program and it does not require users to write complex descriptors before starting a search. Based on sequence alignment and secondary structure, it automatically infers a statistical "secondary structure profile" (SSP), which is then matched against any target database, finding solutions and their associated scores. Source:http://tagc.univ-mrs.fr/erpin/

Hairpin Ribozyme
No additional information available.


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

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