- Transcript BART1_0-u33573.003
- Transcript IDBART1_0-u33573.003
- Gene IDBART1_0-u33573
Barley RTD
Exon Structure of BART1_0-u33573.003
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 84450462 | 84450113 | + |
| chr5H | 2 | 84450961 | 84450535 | + |
| chr5H | 3 | 84451442 | 84451355 | + |
| chr5H | 4 | 84451613 | 84451552 | + |
| chr5H | 5 | 84451927 | 84451787 | + |
| chr5H | 6 | 84462409 | 84461529 | + |
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 | 0.0275654 | 1.11686 | 1.17241 |
| morex | ETI | 0.303232 | 0.282473 | 0.51866 |
| morex | LEA | 0 | 0.0345517 | 0.252454 |
| morex | EPI | 0.109735 | 0 | 0.686352 |
| morex | ROO | 0.180687 | 0 | 0 |
| morex | ROO2 | 0 | 0.340169 | 0.30674 |
| morex | NOD | 0.0679801 | 0 | 0 |
| morex | RAC | 0 | 0 | 0.507839 |
| morex | INF1 | 1.09403 | 0 | 0 |
| morex | INF2 | 2.88235 | 2.30372 | 1.00438 |
| morex | CAR5 | 0.731897 | 0.134889 | 0.662007 |
| morex | CAR15 | 0 | 0 | 0.387008 |
| morex | LEM | 0 | 0.294679 | 0 |
| morex | LOD | 0.323816 | 0.324929 | 0 |
| morex | PAL | 0.566082 | 0 | 0.0703553 |
| morex | SEN | 0 | 0 | 0 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os03g38740.1 | +1 | 6e-113 | 370 | 181/261 (69%) | protein|Dicer, putative, expressed |
| TAIR PP10 | AT3G03300 @ ARAPORT AT3G03300.3 @ TAIR |
+1 | 2e-78 | 272 | 137/251 (55%) | Symbols: DCL2 | dicer-like 2 | chr3:768020-774833 REVERSE LENGTH=1388 |
| BRACH PP3 | Bradi1g15440.3.p | +1 | 1e-140 | 437 | 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 (1949 bp)
>BART1_0-u33573.003 1949 150831_barley_pseudomolecules CAAACGGCAATGGTCCCGAGCGGGTCTCCTCCCTTCCCCCCACTTCCTTTCGAGTCAAAA GGTGAACCCGAAGCGAAGCGGCCAAGCAGCAAAACCTTCGCCCCTAAGCTCACCAAATCA AACCCCACGAGCGCTCGACACAGATTCACCCGTGCGCCTCGGCAGCAGCCCAAGCGTACT CGCCGCCTCCGCCGCCTCGCTGCCGCCGCGCCGCCGATTTCGTTCTCGCGCCAGCCCAGA ATCTCATCAGACACCACCATGGATGCCGCCGCCGCCGCCGCCCCCCCCGCCGCGGACTCA GCCGTGACAGAGGAAGCACACAAGGAGGATCCGGAGATCGTAGCGAGATGGTACCAGCTG GAGGCGCTGGAGCGGGCCATGAGCGGGAACACGGTGGCTTTCCTGGATACGGGGGCCGGG AAGACGCTCATCGCGGGGTTGCTGCTGCGCGCCTACGCGCACCTCGTGCGGAAGCCGGCG CGGGAATTCGCCGTCTTCCTCGTCCCCACCCGCGTGCTCGTGGAGCAGCAGGCACGGGTC GTCGAGGCGCATACCGACCTCCGCGTCTCCAAGTTCACCGGCGACATGGGCGTCGACTTC TGGGACGCCGCAATCTGGCGCCGCGTGGTGGACGACGCCGAGGTGCTTGTCATGACGCCG CAGATCCTCCTCGACAACCTCCGACACAGCTTCTTCCGCCTCCAGGACATCGCGTTGCTC ATCTTCGACGAGTGCCACCGCGCCAAGGGCAACTCCCCGTATGCGTGCATTCTCAAGGAA TTCTACCACCCTGTAATGAATTCTAGACCACGGGGCCCTCTGCCGAGGATATTTGGGATG ACTGCTTCGCCCACAGATGCAAAAAATCAGCTGCAAGAGAGCTATTCCAAACGAATCGTC GAACTGGAGAATCTATTGAACTCAAAGGTGTACACAGTTGACAATGAATCGGCTTTATCG GAATATATACCATTTGCCACTACGAGGATTGTGGAGTACGATGATTCTATCATCCCATCC AACTCACATAACCATATTAACAGTTGTTTGGACAGGTTGCAAGAGAAGGACAACAACACC CTCTAAGATGTGTTTCCCAGGCATAAACGCCGTCTGCATCGGTTGGACTACTGAATGAGC TATCTTCGTCAACCTATTCGTGCCAACCTTTGTAGAAAATTTGAAGCTGACATTGAGCAA ACATATCGGTCTGAACTGCTCAATGCGTACAACCTCCGCCTTCTTTGGCAACAACGTGAT TGTTCCAAAGTTAAGGTGGAATAGCTGTAACTGGCCATTAAATAAATCATGGAACATAGG CAACATATCCCCCTTAATGATATGCTAGCATTTTTTTTATAAAATTCCGCTGGAAACCCG TCTGGCTCCGGTGCCTTATTTTGTTTGTTTGTGCTATTGAGTCGTACACCTCCTTCTCGG TAGATGGAGCTGATAGCATCTCATTCTCATCTGAATTGAGTTGAGGTATATCATGAGTTG TGCTTTCATCCAAAGTGACCAAATAATTTCTTGCAATATTCAGAGATATATAATTTGAAG TTCTCGTGACCTACTATTGTTCCTTCGTCTTGCTCAAGTTGGGCTATTTTTTCTTTCGAT GTTTGCCGTTTGCAATCATGTGAAAGAATTGAGTGTTATCGTCCCCATGAACGACCTTTG TCACCTTAGCTCGAAGTGCCCATTTCACCTCCTCTTCTCTCAAAAGTTTTTGCAAATTCT TCTCAGCTTCAATCTTGTTATTCCTATAAGTCAGATTGAGATGAGCAGACTCAGCTTTCA CATCTAATTCATCAATTAGACGAATGAGTCTTTCTTTTTCTATTATATATATATCGCTTT GATTTTTCGCCCATCCTCTCAAGAACTGGCGCAAGCGTCGGATTTTGTTTTGCCATCTTT CTATATTCGTAGATCCACCTGAATCCCTA
Protein Sequence (361 aa)
>BART1_0-u33573.003 361 150831_barley_pseudomolecules QTAMVPSGSPPFPPLPFESKGEPEAKRPSSKTFAPKLTKSNPTSARHRFTRAPRQQPKRT RRLRRLAAAAPPISFSRQPRISSDTTMDAAAAAAPPAADSAVTEEAHKEDPEIVARWYQL EALERAMSGNTVAFLDTGAGKTLIAGLLLRAYAHLVRKPAREFAVFLVPTRVLVEQQARV VEAHTDLRVSKFTGDMGVDFWDAAIWRRVVDDAEVLVMTPQILLDNLRHSFFRLQDIALL IFDECHRAKGNSPYACILKEFYHPVMNSRPRGPLPRIFGMTASPTDAKNQLQESYSKRIV ELENLLNSKVYTVDNESALSEYIPFATTRIVEYDDSIIPSNSHNHINSCLDRLQEKDNNT L