Schema for Drosophila RefSeq Transcripts - BLAT Alignment of Drosophila RefSeq Transcripts
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Database: DanaCAF1 Primary Table: RefSeqRNA_DgriRefSeq2 Row Count: 24,493   Data last updated: 2022-10-20
field | example | SQL type | info |
bin | 585 | smallint(5) unsigned | range |
chrom | scaffold_10103 | varchar(255) | values |
chromStart | 509 | int(10) unsigned | range |
chromEnd | 3453 | int(10) unsigned | range |
name | XM_001991192 | varchar(255) | values |
score | 442 | int(10) unsigned | range |
strand | - | char(1) | values |
thickStart | 518 | int(10) unsigned | range |
thickEnd | 3453 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 10 | int(10) unsigned | range |
blockSizes | 150,3,87,210,195,96,29,810,... | longblob | |
chromStarts | 0,191,203,329,889,1144,1259... | longblob | |
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
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585 | scaffold_10103 | 509 | 3453 | XM_001991192 | 442 | - | 518 | 3453 | 0 | 10 | 150,3,87,210,195,96,29,810,562,209, | 0,191,203,329,889,1144,1259,1305,2115,2735, |
585 | scaffold_10103 | 509 | 3453 | XM_032738037 | 442 | - | 518 | 3453 | 0 | 10 | 150,3,87,210,195,96,29,810,562,209, | 0,191,203,329,889,1144,1259,1305,2115,2735, |
585 | scaffold_10187 | 517 | 690 | XR_006246797 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
585 | scaffold_10187 | 517 | 690 | XR_006246767 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
585 | scaffold_10187 | 517 | 690 | XR_006246864 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
585 | scaffold_10187 | 517 | 690 | XR_006246794 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
585 | scaffold_10187 | 517 | 690 | XR_006246786 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
585 | scaffold_10187 | 517 | 690 | XR_006246776 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
585 | scaffold_10187 | 517 | 690 | XR_006246766 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
585 | scaffold_10187 | 517 | 690 | XR_006246622 | 1000 | - | 517 | 517 | 0 | 1 | 173, | 0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Drosophila RefSeq Transcripts (ncbiDrosRefSeq) Track Description
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Description
Drosophila transcripts from the NCBI RefSeq database were aligned against the D. ananassae DanaCAF1 assembly using
BLAT. The thicker boxes denote the coding regions within the transcripts and the thinner boxes denote the untranslated regions.
Methods
RefSeq transcripts were mapped against the D. ananassae
genome assembly using BLAT with the following parameters:
-repeats=lower -q=rnax -t=dnax -mask=lower
The transcript alignments are analyzed by pslReps using the following parameter:
-minAli=0.25
The alignments are then filtered by pslCDnaFilter using the following parameters:
-minId=0.35 -minCover=0.15 -localNearBest=0.010 \
-minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap
References
Kent WJ. BLAT — the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.
The transcripts were obtained from the NCBI FTP site under the following RefSeq assembly accession numbers:
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