- Transcript BART1_0-u42525.006
- Transcript IDBART1_0-u42525.006
- Gene IDBART1_0-u42525
Barley RTD
Exon Structure of BART1_0-u42525.006
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22229409 | 22229231 | + |
| chr6H | 2 | 22229650 | 22229501 | + |
| chr6H | 3 | 22229842 | 22229786 | + |
| chr6H | 4 | 22231287 | 22231195 | + |
| chr6H | 5 | 22231497 | 22231365 | + |
| chr6H | 6 | 22232507 | 22232423 | + |
| chr6H | 7 | 22233100 | 22233048 | + |
| chr6H | 8 | 22233288 | 22233205 | + |
| chr6H | 9 | 22233733 | 22233388 | + |
| chr6H | 10 | 22234371 | 22233825 | + |
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 | 3.94378 | 1.0414 | 1.25177 |
| morex | LEA | 0 | 0.255004 | 0 |
| morex | EPI | 2.44486 | 1.1483 | 0 |
| morex | ROO | 0 | 0.291285 | 0.118429 |
| morex | ROO2 | 0 | 0.209829 | 0 |
| morex | NOD | 0 | 0 | 0.448554 |
| morex | RAC | 0.422825 | 0.586967 | 0 |
| morex | INF1 | 0.470239 | 0.578901 | 0 |
| morex | INF2 | 0.998973 | 0.905898 | 0 |
| morex | CAR5 | 0 | 1.40456 | 0 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 0.495871 | 0.237858 | 0.441575 |
| morex | LOD | 0 | 0 | 0 |
| morex | PAL | 0 | 0 | 0.537483 |
| morex | SEN | 2.11564 | 1.83737 | 0 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03050.1 | +1 | 2e-84 | 251 | 121/144 (84%) | protein|dimethyladenosine transferase, putative, expressed |
| TAIR PP10 | AT1G01860 @ ARAPORT AT1G01860.1 @ TAIR |
+1 | 3e-71 | 207 | 99/155 (64%) | Symbols: PFC1 | Ribosomal RNA adenine dimethylase family protein | chr1:304439-306275 REVERSE LENGTH=343 |
| BRACH PP3 | Bradi3g02232.4.p | +1 | 8e-111 | 272 | 132/144 (92%) | pacid=32819652 transcript=Bradi3g02232.4 locus=Bradi3g02232 ID=Bradi3g02232.4.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 (1727 bp)
>BART1_0-u42525.006 1727 150831_barley_pseudomolecules CGTCTCCGGCCACGCCTCCTCACCGCCGGCCGCCGCCGCCCCGCGGCCGTATCCGGCCCA CATCCGCCGTCGCAACGGCCGCATCCGACGGCGGCGGCGCGGGCGACGACTACCACTCGA CCATCCGCTCACTCAACTCGCACGGCCGCCGCCACGTCCCCCGCAAATCCCTCGGTCAGA ACTACATGCTGAACGCGAGGGTGAACGAGGAGCTGGTGGCGGCGGCGGGGGTAGAGGTAG GGGACGTCGTGCTCGAGATAGGACCCGGGACGGGCTCGCTCACCGCCGCTCTGCTCGCCG CCGGCGCCACCGTCGTCGCCGTCGAGAAGGATAAGCATATGGCTACACTTGTGAGAGATA GGTTTGGATCCACAGAGCAATTGAAGGTCATTGAAGAAGATATTACAAAATTTCACGTTC ACTCCCATTTTCTCCCTATCCTGGACGAGAAATCCCGTGGCACGAAAAAATATGCCAAGG CGGTCTTGTGTCCACCTCAAACTTTGTATTTTGCAGGTTGTAGCAAACTTACCATTCAAT GTCAGCACTGAAGTTGTCAAACAAATTCTCCCAATGGGAGATGTTTTCTCTGTCATGGTG CTCATGCTTCAGGATGAAGCAGCGCTACGCCTTGCAAATGCTTCAATACAAACACCAGAG TACCGACCTATCAATGTGTTTGTGAATTTCTACTCTGAACCCGAATACAAGTTCAAGGTA GAGAGGGCCAACTTTTTCCCTCAACCGACGGTTGACGGTGGTGTTATAAGGTTTAAAATA AAGGATGCTGGGGAGTATCCGCCTGTTAGTTCTAACAAAAGTTTTTTTTCAATGGTGAAC TCCGCGTTCAATGGGAAGCGCAAGATGCTTCGGAAATCACTTCAACACCTATATTCTTCT GTTGAAATCGAGGCCGCTCTTACCAATATCGGTCTTCCGCCTACAGTAAGCTCTCCCTCC ATCCATCCATCCTTGCTCGTGCACTAAATTCATTATTGCTGCAGGCTAGACCGTCGGAAC TGATGATGGATGATTTCGTGAGGTTGCACAATCACCTGGGAAAAGTATGACCACCCCTGC ATTCAAAATGCGTATGGAATCATCTTATTGGTTTGCTCGCTGGACTATGCATGCCTCTGA AGTGATTTTGTTCCCAGCTAGAGGGCACTGCAACTTGCAGATCATCCTTGCTGACAGTGA CCGCCTAGTATTCTTCAGCAGTCCCACAGCCTTCACCGCAACATAATTGGTGGCACAGCT TCAGCCCACGGTGTCCTTGCATGGATGATCATAGTGATTGTGCTATAAGTTCAAAACCAA TGATAATGCGCAGGGCATGATTTGCTCGCACAAGAATTGCAGTTCTTTTCCTTATCGCAG ATAGCATCCCTGCAAGAGGGAAGATACGCGGGCGTTGCATGTGTATAATTTACTGCAACT ATCTATCCTCTTGTACTAATCTTCGCAGGTTGGAGGCAGAAATGTAGGGATCAAATGTCT GTCAGAACAATCTGAAGACCAGGCAAAGATGCTAGCTGCTCATAGTAAATTGCCAATAGC GTTTTTATGTGTGGACATAGATGGTAGATAGAGGTACAGCCATTGCATTTTGAGCTTAAG TTTTGGCTATAAACTGCAACAAAAAGGTGCAAATGCTCAGTGTTTGAGTGAGCGATATTC TGCTGTTTTTTTACCTGGCAGCGTGTCGCTACGATGCAACATATAGT
Protein Sequence (182 aa)
>BART1_0-u42525.006 182 150831_barley_pseudomolecules SPATPPHRRPPPPRGRIRPTSAVATAASDGGGAGDDYHSTIRSLNSHGRRHVPRKSLGQN YMLNARVNEELVAAAGVEVGDVVLEIGPGTGSLTAALLAAGATVVAVEKDKHMATLVRDR FGSTEQLKVIEEDITKFHVHSHFLPILDEKSRGTKKYAKAVLCPPQTLYFAGCSKLTIQC QH