- Transcript BART1_0-u42835.008
- Transcript IDBART1_0-u42835.008
- Gene IDBART1_0-u42835
Barley RTD
Exon Structure of BART1_0-u42835.008
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 34891732 | 34891715 | + |
| chr6H | 2 | 34892153 | 34891929 | + |
| chr6H | 3 | 34892472 | 34892398 | + |
| chr6H | 4 | 34893434 | 34893231 | + |
| chr6H | 5 | 34894042 | 34893848 | + |
| chr6H | 6 | 34894525 | 34894361 | + |
| chr6H | 7 | 34895187 | 34894938 | + |
| chr6H | 8 | 34896103 | 34895891 | + |
| chr6H | 9 | 34896414 | 34896192 | + |
| chr6H | 10 | 34897312 | 34896755 | + |
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 | 0 | 0 |
| morex | ETI | 1.4903 | 1.40383 | 1.4782 |
| morex | LEA | 0 | 0.000129311 | 0.687575 |
| morex | EPI | 5.20262 | 2.49851 | 3.11818 |
| morex | ROO | 0.000000427332 | 0.366467 | 0 |
| morex | ROO2 | 0.598118 | 0.888075 | 1.67898 |
| morex | NOD | 1.0912 | 0 | 0 |
| morex | RAC | 1.06222 | 0.000154629 | 2.04124 |
| morex | INF1 | 0 | 2.90333 | 0 |
| morex | INF2 | 2.15342 | 1.3755 | 1.70735 |
| morex | CAR5 | 0.76742 | 0 | 1.58288 |
| morex | CAR15 | 0.327811 | 0.364195 | 0.83977 |
| morex | LEM | 0.0492831 | 0.607681 | 0 |
| morex | LOD | 0.0000772406 | 0.096001 | 1.43775 |
| morex | PAL | 0.00000140832 | 0 | 1.18164 |
| morex | SEN | 0.54076 | 0.739515 | 0.979793 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03690.1 | +2 | 0.0 | 451 | 208/237 (88%) | protein|beta-amylase, putative, expressed |
| TAIR PP10 | AT5G45300 @ ARAPORT AT5G45300.1 @ TAIR |
+1 | 5e-171 | 325 | 168/299 (56%) | Symbols: BMY2, BAM8 | beta-amylase 2 | chr5:18353636-18356696 FORWARD LENGTH=689 |
| BRACH PP3 | Bradi3g02800.4.p | +1 | 0.0 | 530 | 266/293 (91%) | pacid=32818289 transcript=Bradi3g02800.4 locus=Bradi3g02800 ID=Bradi3g02800.4.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 (2126 bp)
>BART1_0-u42835.008 2126 150831_barley_pseudomolecules CCTCCCCCGGCCCAATTCGGTGCTTTCCAGGCCACTTCTCTGGAAACCCCAGTTTTTACC AACTCTCTGAACAGCTATGCCGTTGGGACGCCATTAGATTCCCAGGCTTCAGCCCTACAA ACAGATGATAGCCTGTCACCGTCGTCATTGGACTCAGTCGTGGTGGCAGAGCAATGCATA AAGAATGAGAGCTTTGGGAATTCAAGTTCAGCCAATTCTTTGAACTGTATGGGTAGTGAT CAGCTATTGAGAGCATCAGCAGTATGGGCGGGTGATTACACGAAAACTCCATATATACCA TTGTACGCCTCTTTGTCTATGGGCATTATCAATTGTTATTGCCAACTGGTTGATCCTGAG GCTGTACGTGCTGAACTAAGGCATCTGAAATCTTTGAATGTTGATGGAGTTATTGTTGAC TGTTGGTGGGGGATTGTAGAAGCCTGGACTCCTCAAAAGTATGAATGGTCTGGCTACAGG GACCTTTTTGGTATCATTAAAGAGTTCAAGCTAAAAGTTCAGGTTGTGTTATCATTTCAT GGGTCTGGGGAGTGTGGATCTGGTCCTGTGTTAATTGCTCTTCCTAGGTGGGTAATGGAA ATTGCACAAGAGAACCAAGATATATTTTTTACCGATCGAGAAGGTAGGAGGAATACAGAA TGCCTCTCCTGGGGAATTGACAAAGAGCGTGTCCTTCGAGGGAGAACTGGCATCGAGGTT TATTTTGATTTCATGAGGAGCTTTCATATGGAATTCAGAACCCTATCTGAAGAGGGTCTT ATTTCTGCTATTGAGATTGGATTGGGTGCTTCTGGAGAGCTAAGATACCCTTCGTGTTCA GAAAAAATGGGCTGGAGATATCCTGGTATTGGTGAGTTTCAGGTATATGCAAAAGAACCT ACGGCAATCAGCCTTGACACGGGGGCATTTGTTTTGGGCCCGTGGGCCTGATAATGCTGG CTACTATAATTCAAGGTCACACGAGACTGGCTTTTTTTGTGACGGAGGTGATTATGACAG CTACTATGGGCGGTTCTTCCTTAATTGGTATTCTGGAATCCTTATAGATCATGTGGATCA GGTGCTCTCACTTGCTACTCTTGCATTTGATGGAGCAGCAGTTGTGGTGAAGATCCCCTC CATCTATTGGTGGTACAGAACTGCAAGCCATGCTGCAGAGCTTACTGCAGGATTCTACAA CCCTACAAATCGAGATGGATACTCTCCAGTTTTCAGAATGCTCAAGAAGCATTCCATAAT TCTTAAAGTGGTTTGTTATGGCCCAGAATTTACAGTTCAGGAGAATGATGAAGCACTTGC TGATCCAGAAGGTTTAACCTGGCAGGTTATGAACGCAGCATGGGATCATGGTCTATCTGT AAGTGTAGAGAGTGCTCTTCCATGTCTTGACGTGGACATGTACTCTCGGATCCTTGACAC AGCAAAGCCGAGGAATGATCCTGACCGACACCATCTCTCATTCTTTGCATACCGTCAGCG AACTCCATTCCTTTTGCAGAGAGATGTGTGCTTCTCAGAGCTTGAGACCTTCGTAAAGTG TATGCACGGGGAGGCTATCCAGAACTTTGTAGATTGAACTTGCTTTGGCGACGCATTCCC TGTTATGTTGCAGCTCGCGTTCTGCAAATTTCCGGATTCCCTGCGTAGCTATCACAAGCT TTAACTCATATTGCTGATTGCTGCGTTCCGGCCATCCCCGCCTTTGCTATGGGTCAGCTA ACCAGATGGCACTGAAACTGTTGTGCTGGTGGTGGGCAAGGATTAGCATCCCTTATCTGT GGTACAGGGCTGATAGTTCAGCAAGTTTTTACCGTGGTGTGACCTAGCTTGGGCTAGAAA GATGGAAAGAATGGCGATGTATATATCTAATAGTACTACACTATCATGCTCTAAGATGCA AAGAAAGCGTCTGAATTCTCCATGGTAAGCTGCTCGATGACAAGTGCTTGCAGTGGGTTT CCGAGGGATTCCTTGAACTCGCTTTTCCCTTTCTATTTTCCTTTGAACCTTATTGGGACA TTTGTATTTCCGTTATGAAAGTAATGGAAAGGGGTTATGCCCAGCTCAAAAAAAAATAAA ATCTCCATGATGCCGAAACATCTTTC
Protein Sequence (316 aa)
>BART1_0-u42835.008 316 150831_barley_pseudomolecules PPPAQFGAFQATSLETPVFTNSLNSYAVGTPLDSQASALQTDDSLSPSSLDSVVVAEQCI KNESFGNSSSANSLNCMGSDQLLRASAVWAGDYTKTPYIPLYASLSMGIINCYCQLVDPE AVRAELRHLKSLNVDGVIVDCWWGIVEAWTPQKYEWSGYRDLFGIIKEFKLKVQVVLSFH GSGECGSGPVLIALPRWVMEIAQENQDIFFTDREGRRNTECLSWGIDKERVLRGRTGIEV YFDFMRSFHMEFRTLSEEGLISAIEIGLGASGELRYPSCSEKMGWRYPGIGEFQVYAKEP TAISLDTGAFVLGPWA