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Tables and columns in the TAG database

(1) Good_Matches: This is the main table contains most of the EST alignment information. 
Columns:        alignID         each EST alignment has a specific ID. 
                Genome/gi/start/stop    self explanatory, indicating ESTgi aligned to which region of chromosome/BAC
                Gont/Qont       orientation of the alignment on Genome/Query cDNA
                Similar         similarity of the alignment
                length          length of the match region
                Cov             Coverage of the match region on the cDNA
                isCognate       Is this an Cognate alignment? True means that this is the best alignment for the cDNA.
                SeqType EST or cDNA, or cross-species EST
                PGS             Predicted Gene Structure, including coordinates for each intron/exon
                GeneStructure   Length for the predicted intron/exon

(2)SIfull: This is the main table hold all special intron (alternative splicing events) information. 
Columns:        alignID         Which EST alignment the special intron come from
                IntronID        The ID of special intron (or exon in ExonS case, will be changed in newer version)
                Genome/Lstart/Lstop/len  self explanatory
                Ecnt            EST counts supporting the intron
                gi              A representative EST supporting the intron
                Dscore/Ascore   Donor/Acceptor site score predicted by GeneSeqer
                AltID           The ID for alternative special intron (or exon in IntronR and ExonS case)
                AltGi/AltEcnt   A representative EST/EST counts supporting the AltID
                SItype          Special intron type. 
                hostIntron      The assumed constitutively spliced introns. Meaningful only for AltD/A/P events
                geneID          Which gene does the special intron belongs to
                SIid            ID for the special intron / AS events
                SItypeF         Simple version for SItype. Different with the SItype only in AltD/A/P events.

(3) TAGenes: The expressed gene list. Most columns are self explanatory.
                Txn             The count of transcription support for the gene. 
                Note: if an EST cluster is in a novel region or different orientation with the annotated gene, 
                        it may be named as "TC_XXXX".

(4) TAGexons: The high quality exon list. 
Columns:        alignID         Which EST alignment the exon is originally from.
                num             The order of exons in the original alignment. 
                Qstart/Qstop/Lstart/Lstop       Coordinates of the exon on Query or Genome
                score           Similarity score for the exon alignment
                Genome/gi       self explanatory
                Ecnt            EST count supporting the exons
                exonCNT         How many exons does the origin alignment have.
                ExonP           Position of the exon in the alignment (First/Medium/Last). 
                                In some case, the positions are changed after merging with other exons. 
                Include         How many compatible exons are merged with this exon
                ExonID          The unique exon identification

(5) TAGintrons: The high quality exon list.
Columns:        alignID         Which EST alignment the intron is originally from.
                gi/Genome/Lstart/Lstop/len      self explanatory                        
                num             The order of introns in the original alignment. 
                Dscore/Ascore   Donor/Acceptor site score predicted by GeneSeqer
                UEsim/DEsim     similarity for 50bp Upstream/Downstream exons flanking the intron
                IntronID        The unique intron identification


(6) eTrans: the electronic transcript sequence coordinates. 
                This table is used to show the theoretical combination of compatible introns/exons. 
                They corresponding to the green bar/lines in the webpage when you click "eTranscript". 
Columns:        clustID         EST cluster ID
                eID             if an EST cluster has multiple eTrans, they will be numbered accordingly.
                                 "s" means single exon eTrans
                Genome/TFrom/TTo/TLen   transcript starting/ending position/length on which Chr/BAC
                ExonIntron      The ExonID and  IntronID used to generate this eTrans
                Transcript      coordinates on genome for the corresponing intron/exon structure
                Gene structure  Length for each exon/intron
                INum            Number of introns on the eTrans
                AALen           the coded peptide length
                Frame           which translation frame
                tATG/tTAA       start and stop codon on the eTrans cDNA  
                CDStart/CDStop  start and stop codon on the genome coordinates. 
                        Note:   the minus number means that there is no real stop codon, 
                                the eTrans sequences has ended. (open triangle in the graph)
                SI      special intron/alternative splicing events on this eTrans

(7) gbk_gene_annotation: the table held gene annotation (not necessarily from genbank).
                Most column names should be self explanatory or similar to the ones in eTrans table.
                block1 or block2 columns if any are used for speed up query process only. 
                The gene annotation is shown as blue bars in the graph. 

          

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