Schema for TransDecoder Transcripts - Transcripts and Coding Regions Predicted by TransDecoder |
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Database: DereCAF1 Primary Table: transdecoder Row Count: 11,766 Data last updated: 2022-10-20
| field | example | SQL type | info |
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| bin | 585 | smallint(5) unsigned | range |
| name | DereCAF1_stringtie.15.1_m.2 | varchar(255) | values |
| chrom | scaffold_1230 | varchar(255) | values |
| strand | - | char(1) | values |
| txStart | 255 | int(10) unsigned | range |
| txEnd | 834 | int(10) unsigned | range |
| cdsStart | 255 | int(10) unsigned | range |
| cdsEnd | 638 | int(10) unsigned | range |
| exonCount | 2 | int(10) unsigned | range |
| exonStarts | 255,423, | longblob | |
| exonEnds | 367,834, | longblob | |
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Sample Rows
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| bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds |
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| 585 | DereCAF1_stringtie.15.1_m.2 | scaffold_1230 | - | 255 | 834 | 255 | 638 | 2 | 255,423, | 367,834, |
| 585 | DereCAF1_stringtie.16.1_m.3 | scaffold_1246 | + | 432 | 1026 | 432 | 1026 | 1 | 432, | 1026, |
| 585 | DereCAF1_stringtie.16.1_m.4 | scaffold_1246 | + | 432 | 1026 | 432 | 1026 | 1 | 432, | 1026, |
| 585 | DereCAF1_stringtie.22.1_m.7 | scaffold_1247 | - | 23 | 1233 | 244 | 1231 | 2 | 23,831, | 375,1233, |
| 585 | DereCAF1_stringtie.22.2_m.8 | scaffold_1247 | - | 23 | 1233 | 244 | 1231 | 2 | 23,603, | 375,1233, |
| 585 | DereCAF1_stringtie.17.1_m.9 | scaffold_1255 | + | 206 | 1227 | 206 | 1226 | 2 | 206,504, | 411,1227, |
| 585 | DereCAF1_stringtie.30.1_m.20 | scaffold_1388 | + | 0 | 2594 | 0 | 1205 | 2 | 0,938, | 663,2594, |
| 585 | DereCAF1_stringtie.30.1_m.21 | scaffold_1388 | + | 0 | 2594 | 1448 | 1817 | 2 | 0,938, | 663,2594, |
| 585 | DereCAF1_stringtie.30.2_m.19 | scaffold_1388 | + | 0 | 9087 | 0 | 8968 | 2 | 0,8701, | 663,9087, |
| 585 | DereCAF1_stringtie.31.1_m.14 | scaffold_1388 | - | 1644 | 5837 | 4829 | 5219 | 8 | 1644,2364,2658,2867,3159,3924,4511,4658, | 2309,2595,2806,3100,3868,4450,4598,5837, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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TransDecoder Transcripts (transdecoder) Track Description
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Description
This track shows the RNA-Seq transcripts assembled by StringTie. Coding regions within the transcript are identified by TransDecoder.
The RNA-Seq data were obtained from the NCBI Sequence Read Archive under the BioProject accession numbers
PRJNA264407 (ovarian follicle cells; Chirn GW et al., 2014) and
PRJNA414017 (adult males; Ma S et al., 2018).
Methods
TransDecoder was run against the transcripts assembled by StringTie using default parameters. The open reading frames predicted by TransDecoder were searched against the Swiss-Prot database using NCBI blastp and against the Pfam database using HMMER. Open reading frames are kept if they satisfy the TransDecoder.Predict filtering criteria or if they show significant matches to either Swiss-Prot or Pfam.
References
Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN.
Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity.
Aging Cell. 2018 Apr 19:e12740.
Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC.
Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals.
PLoS Genet. 2015 Nov 20;11(11):e1005652.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL.
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Nat Biotechnol. 2015 Mar;33(3):290-5.
Haas BJ et al.
De novo transcript sequence reconstruction
from RNA-seq using the Trinity platform for reference generation and analysis.
Nat Protoc. 2013 Aug;8(8):1494-512.
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