- Transcript BART1_0-u33573.002
- Transcript IDBART1_0-u33573.002
- Gene IDBART1_0-u33573
Barley RTD
Exon Structure of BART1_0-u33573.002
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 84450462 | 84450113 | + |
| chr5H | 2 | 84450961 | 84450535 | + |
| chr5H | 3 | 84451442 | 84451355 | + |
| chr5H | 4 | 84451613 | 84451518 | + |
| chr5H | 5 | 84451927 | 84451787 | + |
| chr5H | 6 | 84461529 | 84461517 | + |
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 | 0.538851 | 2.43734 | 2.67295 |
| morex | ETI | 2.48645 | 3.14215 | 4.79255 |
| morex | LEA | 3.74867 | 0.510915 | 0.925129 |
| morex | EPI | 1.72501 | 2.64961 | 3.18021 |
| morex | ROO | 0.450776 | 0.776213 | 0 |
| morex | ROO2 | 3.39114 | 2.6533 | 3.2307 |
| morex | NOD | 0.662444 | 2.92258 | 1.62272 |
| morex | RAC | 7.7083 | 8.43086 | 6.92399 |
| morex | INF1 | 7.40457 | 5.39565 | 6.72714 |
| morex | INF2 | 13.4671 | 11.2836 | 10.7729 |
| morex | CAR5 | 6.18069 | 6.90177 | 2.30289 |
| morex | CAR15 | 3.62171 | 1.29721 | 3.22822 |
| morex | LEM | 3.59107 | 2.20861 | 3.78515 |
| morex | LOD | 6.40516 | 5.22185 | 1.94246 |
| morex | PAL | 5.434 | 3.61553 | 4.75984 |
| morex | SEN | 1.39971 | 1.8217 | 0.675649 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os03g38740.1 | +1 | 2e-86 | 286 | 141/204 (69%) | protein|Dicer, putative, expressed |
| TAIR PP10 | AT3G03300 @ ARAPORT AT3G03300.3 @ TAIR |
+1 | 2e-68 | 224 | 109/182 (60%) | Symbols: DCL2 | dicer-like 2 | chr3:768020-774833 REVERSE LENGTH=1388 |
| BRACH PP3 | Bradi1g15440.3.p | +1 | 4e-116 | 331 | 153/186 (82%) | 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 (1115 bp)
>BART1_0-u33573.002 1115 150831_barley_pseudomolecules CAAACGGCAATGGTCCCGAGCGGGTCTCCTCCCTTCCCCCCACTTCCTTTCGAGTCAAAA GGTGAACCCGAAGCGAAGCGGCCAAGCAGCAAAACCTTCGCCCCTAAGCTCACCAAATCA AACCCCACGAGCGCTCGACACAGATTCACCCGTGCGCCTCGGCAGCAGCCCAAGCGTACT CGCCGCCTCCGCCGCCTCGCTGCCGCCGCGCCGCCGATTTCGTTCTCGCGCCAGCCCAGA ATCTCATCAGACACCACCATGGATGCCGCCGCCGCCGCCGCCCCCCCCGCCGCGGACTCA GCCGTGACAGAGGAAGCACACAAGGAGGATCCGGAGATCGTAGCGAGATGGTACCAGCTG GAGGCGCTGGAGCGGGCCATGAGCGGGAACACGGTGGCTTTCCTGGATACGGGGGCCGGG AAGACGCTCATCGCGGGGTTGCTGCTGCGCGCCTACGCGCACCTCGTGCGGAAGCCGGCG CGGGAATTCGCCGTCTTCCTCGTCCCCACCCGCGTGCTCGTGGAGCAGCAGGCACGGGTC GTCGAGGCGCATACCGACCTCCGCGTCTCCAAGTTCACCGGCGACATGGGCGTCGACTTC TGGGACGCCGCAATCTGGCGCCGCGTGGTGGACGACGCCGAGGTGCTTGTCATGACGCCG CAGATCCTCCTCGACAACCTCCGACACAGCTTCTTCCGCCTCCAGGACATCGCGTTGCTC ATCTTCGACGAGTGCCACCGCGCCAAGGGCAACTCCCCGTATGCGTGCATTCTCAAGGAA TTCTACCACCCTGTAATGAATTCTAGACCACGGGGCCCTCTGCCGAGGATATTTGGGATG ACTGCTTCGCCCACAGATGCAAAAATTCGACCAAATCTGTCACACTATTCCTTCCATAGA TCAGCTGCAAGAGAGCTATTCCAAACGAATCGTCGAACTGGAGAATCTATTGAACTCAAA GGTGTACACAGTTGACAATGAATCGGCTTTATCGGAATATATACCATTTGCCACTACGAG GATTGTGGAGTACGATGATTCTATCATCCCATCCAACTCACATAACCATATTAACAGTTG TTTGGACAGGTTGCAAGAGAAGCGTTTCATGCAGG
Protein Sequence (324 aa)
>BART1_0-u33573.002 324 150831_barley_pseudomolecules QTAMVPSGSPPFPPLPFESKGEPEAKRPSSKTFAPKLTKSNPTSARHRFTRAPRQQPKRT RRLRRLAAAAPPISFSRQPRISSDTTMDAAAAAAPPAADSAVTEEAHKEDPEIVARWYQL EALERAMSGNTVAFLDTGAGKTLIAGLLLRAYAHLVRKPAREFAVFLVPTRVLVEQQARV VEAHTDLRVSKFTGDMGVDFWDAAIWRRVVDDAEVLVMTPQILLDNLRHSFFRLQDIALL IFDECHRAKGNSPYACILKEFYHPVMNSRPRGPLPRIFGMTASPTDAKIRPNLSHYSFHR SAARELFQTNRRTGESIELKGVHS