- Transcript BART1_0-u33573.004
- Transcript IDBART1_0-u33573.004
- Gene IDBART1_0-u33573
Barley RTD
Exon Structure of BART1_0-u33573.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 84450462 | 84450133 | + |
| chr5H | 2 | 84450961 | 84450535 | + |
| chr5H | 3 | 84451442 | 84451355 | + |
| chr5H | 4 | 84451613 | 84451552 | + |
| chr5H | 5 | 84451927 | 84451787 | + |
| chr5H | 6 | 84452323 | 84452006 | + |
grey: non-coding, green: Barley Morex IBSC 2017 Transcript CDS, red: Barley RTD exons
Salmon TPM Values: sixteensamplesmorex
These TPM values were generated by using the RNA-seq data from a 16-tissue experiment in Morex (published here) were calculated using Salmon (version Salmon-0.8.2) using BaRTv1.0-QUASI as the reference transcript dataset. Click here for more information about the RNA-seq experiment and materials
| Sample | Treatment | Rep 1 | Rep 2 | Rep 3 |
|---|---|---|---|---|
| morex | EMB | 0.533555 | 0.950759 | 0.315445 |
| morex | ETI | 1.66439 | 5.87996 | 3.61095 |
| morex | LEA | 0 | 0.814862 | 0 |
| morex | EPI | 0.52902 | 1.55003 | 0.760154 |
| morex | ROO | 0.272022 | 0.96472 | 1.43693 |
| morex | ROO2 | 2.25115 | 1.29905 | 1.82163 |
| morex | NOD | 1.20556 | 0.381217 | 1.1435 |
| morex | RAC | 3.59528 | 4.28219 | 3.32224 |
| morex | INF1 | 0.862928 | 3.28218 | 3.94513 |
| morex | INF2 | 3.47574 | 8.02635 | 7.80184 |
| morex | CAR5 | 3.07911 | 2.95034 | 2.98389 |
| morex | CAR15 | 1.52548 | 2.74334 | 0.161859 |
| morex | LEM | 3.95052 | 3.76121 | 5.11183 |
| morex | LOD | 3.8901 | 1.2293 | 5.45986 |
| morex | PAL | 2.2697 | 4.35127 | 4.45904 |
| morex | SEN | 1.17146 | 1.10966 | 1.03617 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os03g38740.1 | +2 | 2e-115 | 370 | 177/244 (73%) | protein|Dicer, putative, expressed |
| TAIR PP10 | AT3G03300 @ ARAPORT AT3G03300.3 @ TAIR |
+2 | 4e-80 | 270 | 135/242 (56%) | Symbols: DCL2 | dicer-like 2 | chr3:768020-774833 REVERSE LENGTH=1388 |
| BRACH PP3 | Bradi1g15440.3.p | +2 | 1e-142 | 435 | 205/254 (81%) | pacid=32792175 transcript=Bradi1g15440.3 locus=Bradi1g15440 ID=Bradi1g15440.3.v3.1 annot-version=v3.1 |
Barley PseudoMolecules GBrowse
Click here to see more tracks within GBrowse -->
grey: non-coding, green: Barley Morex IBSC 2017 Transcript CDS, red: Barley RTD exons
CDS Sequence (1366 bp)
>BART1_0-u33573.004 1366 150831_barley_pseudomolecules CGGGTCTCCTCCCTTCCCCCCACTTCCTTTCGAGTCAAAAGGTGAACCCGAAGCGAAGCG GCCAAGCAGCAAAACCTTCGCCCCTAAGCTCACCAAATCAAACCCCACGAGCGCTCGACA CAGATTCACCCGTGCGCCTCGGCAGCAGCCCAAGCGTACTCGCCGCCTCCGCCGCCTCGC TGCCGCCGCGCCGCCGATTTCGTTCTCGCGCCAGCCCAGAATCTCATCAGACACCACCAT GGATGCCGCCGCCGCCGCCGCCCCCCCCGCCGCGGACTCAGCCGTGACAGAGGAAGCACA CAAGGAGGATCCGGAGATCGTAGCGAGATGGTACCAGCTGGAGGCGCTGGAGCGGGCCAT GAGCGGGAACACGGTGGCTTTCCTGGATACGGGGGCCGGGAAGACGCTCATCGCGGGGTT GCTGCTGCGCGCCTACGCGCACCTCGTGCGGAAGCCGGCGCGGGAATTCGCCGTCTTCCT CGTCCCCACCCGCGTGCTCGTGGAGCAGCAGGCACGGGTCGTCGAGGCGCATACCGACCT CCGCGTCTCCAAGTTCACCGGCGACATGGGCGTCGACTTCTGGGACGCCGCAATCTGGCG CCGCGTGGTGGACGACGCCGAGGTGCTTGTCATGACGCCGCAGATCCTCCTCGACAACCT CCGACACAGCTTCTTCCGCCTCCAGGACATCGCGTTGCTCATCTTCGACGAGTGCCACCG CGCCAAGGGCAACTCCCCGTATGCGTGCATTCTCAAGGAATTCTACCACCCTGTAATGAA TTCTAGACCACGGGGCCCTCTGCCGAGGATATTTGGGATGACTGCTTCGCCCACAGATGC AAAAAATCAGCTGCAAGAGAGCTATTCCAAACGAATCGTCGAACTGGAGAATCTATTGAA CTCAAAGGTGTACACAGTTGACAATGAATCGGCTTTATCGGAATATATACCATTTGCCAC TACGAGGATTGTGGAGTACGATGATTCTATCATCCCATCCAACTCACATAACCATATTAA CAGTTGTTTGGACAGGTTGCAAGAGAAGGAGTCAGGGTGGACCGTTTCTGATGGATAAGT CTATGTACTATGGTCTTTGTGGGGCTGCAGCACATAGTCCTTTGTGGGGCTGCAGCACAT GGTCCTTGTGGCTGTTCGGATAGAATCCTTGACCATCAAGGACTGGCAGTTAGGATAGCA TCTTAGACTAGCATCTTAGACTAGCATCTTAGCATATGCTTGGCTGGCTAGCAGCCTATA AATATGTATTCCCAACCCCTCAGGTTGGCATGGCATTGTGTGAGAAATAAACCAACGAAA ATTGTCCCAACTCTCCTAGTGTTATCCACAACTATCAATGCTCAGG
Protein Sequence (358 aa)
>BART1_0-u33573.004 358 150831_barley_pseudomolecules GSPPFPPLPFESKGEPEAKRPSSKTFAPKLTKSNPTSARHRFTRAPRQQPKRTRRLRRLA AAAPPISFSRQPRISSDTTMDAAAAAAPPAADSAVTEEAHKEDPEIVARWYQLEALERAM SGNTVAFLDTGAGKTLIAGLLLRAYAHLVRKPAREFAVFLVPTRVLVEQQARVVEAHTDL RVSKFTGDMGVDFWDAAIWRRVVDDAEVLVMTPQILLDNLRHSFFRLQDIALLIFDECHR AKGNSPYACILKEFYHPVMNSRPRGPLPRIFGMTASPTDAKNQLQESYSKRIVELENLLN SKVYTVDNESALSEYIPFATTRIVEYDDSIIPSNSHNHINSCLDRLQEKESGWTVSDG