- Transcript BART1_0-u29736.004
- Transcript IDBART1_0-u29736.004
- Gene IDBART1_0-u29736
Barley RTD
Exon Structure of BART1_0-u29736.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr4H | 1 | 483706263 | 483705903 | + |
| chr4H | 2 | 483706600 | 483706534 | + |
| chr4H | 3 | 483706780 | 483706679 | + |
| chr4H | 4 | 483707382 | 483707226 | + |
| chr4H | 5 | 483712167 | 483711486 | + |
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 | 4.97869 | 5.18148 | 5.37709 |
| morex | ETI | 1.21016 | 0 | 0 |
| morex | LEA | 1.84693 | 0 | 0 |
| morex | EPI | 0.808344 | 0.625124 | 0 |
| morex | ROO | 2.32508 | 3.11783 | 1.20297 |
| morex | ROO2 | 1.72588 | 1.21278 | 2.32929 |
| morex | NOD | 4.52292 | 1.15178 | 0 |
| morex | RAC | 0.898555 | 0.889732 | 2.34137 |
| morex | INF1 | 1.6478 | 0 | 4.77077 |
| morex | INF2 | 1.27367 | 4.22466 | 0 |
| morex | CAR5 | 6.63065 | 4.18321 | 5.45838 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 0 | 0 | 0 |
| morex | LOD | 0 | 1.52829 | 0 |
| morex | PAL | 0 | 0 | 0.674905 |
| morex | SEN | 0 | 1.04042 | 1.17699 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os03g27320.1 | +3 | 9e-146 | 420 | 223/262 (85%) | protein|steroid binding protein, putative, expressed |
| TAIR PP10 | AT5G58220 @ ARAPORT AT5G58220.1 @ TAIR |
+3 | 3e-81 | 254 | 141/260 (54%) | Symbols: TTL | transthyretin-like protein | chr5:23554546-23555861 REVERSE LENGTH=324 |
| BRACH PP3 | Bradi1g60700.1.p | +3 | 1e-152 | 437 | 230/261 (88%) | pacid=32804008 transcript=Bradi1g60700.1 locus=Bradi1g60700 ID=Bradi1g60700.1.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 (1369 bp)
>BART1_0-u29736.004 1369 150831_barley_pseudomolecules ATTCACCTTCGTCTTACCCTTCCGGCAAAAACAGGTGTTGCTCTCGTAGCGCTCGCTCTC ACCCACCCTTCCCCAACTCGCATCCAGCGCCGCAACCCCTCGTCTCTCCCCCCCTTCCGA TCTGAGGCGTCGTTGGAGATCGGCGGCAACCGAAGAGGCGTCCGACGACGGCCGTCGCGG GTGGCACCAGTGCAGTGGAGCAAATCAACCAGTTGAGATGGCGACATTGAGGCCGCTGAG CGTGGAGGAGGTGCTGAGGGTGAACGGCAGCCACCGCTTTGCCGCCGCGCTGGCTGCCGC CTCCCCCTTTGATTCTCTTGCCAACGCGCTCCTTGCCGCCCGCCGCATCTGGCTGAACGA GTCACTACAGGTGGAGCAAGGAAGAGCAATCAGCTGCTCTTTCCACAGCCACTGATTCGA CTGCGCAGGAGTTGTCCGAGTGGAATGCCAAATACAGGGAGAAGTTTGGGTTCGTGTTCA TGATATGCGCATCTGGGAGGACTGCCCCTGAGGTCTTAGCTGAGCTTAAGAGGCGTTATG CAAATAGACCAGTTGTTGAGCTTGAGGCTGCGGCAGAGGAAGAACTGAAGATAACTGAGC TGCGTCTTGCAAAGCTTTTCGCATCAGAAACTGCTGCTCCCCCTACTTCAGGTGAAAATC AGATTAGCCAACCGGATAAAGCAGCAGATCGGATGCGGATTATTGGTGCACACCTTGGAG CTCTTTCCCAGCTTTCTGCCTATAAAGCTCCTGAAATTACAGGCAACTCCAACCGGACAC GCCCTCCTATCACAACCCATGTGCTGGACACGGCTCTTGGATCGCCAGCATCTGGAATTG AAGTTCACCTGGAGATGTGGAAGGACGCGTCAAGTACCCCGTCATTTGACAACAAAGATT TCAAGGGATGGACAACCCTAGGCTCTTCGATTACAAACAATGATGGACGCAGCGGTCAGC TGATGGACATCGTTGACAATGTCACTCCTGGTTTCTACCGCATAAGTTTCAATACCTCCA AGTATGCACCGTCAGGGTTCTTCCCTTACGTGAGCATCATATTTGAGATAAAAAGAAGCC AGGCGACCGAGCATTTCCATGTGCCTCTTTTACATTCTCCTTTTTCCTTTACCACTTACC GTGGCAGCTAAGCTGTCAATTTGTGTGTAAATCACATCGAGTGATGGTATTGTTCTGAAA CAAGCATAAATGGTCGTAAATCAGGGTGTTTAGATGTCACTGACATTGTGATATTTGAAT AATAATGTTCCATGTAATAATAAGCTCGAGTATGCAGTGACATTGGATCAGTTTGTTTTC AATACTTTTATCCATTGCTATTTGTGATTGGGTGGCCTTGAGTGTGGTA
Protein Sequence (223 aa)
>BART1_0-u29736.004 223 150831_barley_pseudomolecules MICASGRTAPEVLAELKRRYANRPVVELEAAAEEELKITELRLAKLFASETAAPPTSGEN QISQPDKAADRMRIIGAHLGALSQLSAYKAPEITGNSNRTRPPITTHVLDTALGSPASGI EVHLEMWKDASSTPSFDNKDFKGWTTLGSSITNNDGRSGQLMDIVDNVTPGFYRISFNTS KYAPSGFFPYVSIIFEIKRSQATEHFHVPLLHSPFSFTTYRGS