- Transcript BART1_0-u42525.004
- Transcript IDBART1_0-u42525.004
- Gene IDBART1_0-u42525
Barley RTD
Exon Structure of BART1_0-u42525.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22229409 | 22229170 | + |
| chr6H | 2 | 22229650 | 22229501 | + |
| chr6H | 3 | 22229842 | 22229786 | + |
| chr6H | 4 | 22231287 | 22231195 | + |
| chr6H | 5 | 22231497 | 22231402 | + |
| chr6H | 6 | 22232507 | 22232423 | + |
| chr6H | 7 | 22233100 | 22233048 | + |
| chr6H | 8 | 22233288 | 22233205 | + |
| chr6H | 9 | 22233733 | 22233388 | + |
| chr6H | 10 | 22234573 | 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 | 0.952159 | 2.50273 | 1.47917 |
| morex | ETI | 15.4394 | 12.9288 | 16.3957 |
| morex | LEA | 4.68137 | 0.413489 | 4.53234 |
| morex | EPI | 3.04619 | 5.12702 | 2.70268 |
| morex | ROO | 0 | 0 | 0 |
| morex | ROO2 | 0 | 0.0738692 | 0.78145 |
| morex | NOD | 0.856971 | 0 | 0.202141 |
| morex | RAC | 1.36578 | 1.44621 | 2.38558 |
| morex | INF1 | 2.39903 | 3.18608 | 2.54421 |
| morex | INF2 | 1.01055 | 2.90086 | 1.76071 |
| morex | CAR5 | 0.795798 | 0.866629 | 2.81142 |
| morex | CAR15 | 0 | 0 | 0.495382 |
| morex | LEM | 3.65081 | 4.23136 | 4.36551 |
| morex | LOD | 0 | 1.03023 | 0 |
| morex | PAL | 2.79002 | 3.93375 | 2.92869 |
| morex | SEN | 24.4784 | 10.3062 | 9.83263 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03050.1 | +1 | 4e-109 | 328 | 159/190 (84%) | protein|dimethyladenosine transferase, putative, expressed |
| TAIR PP10 | AT1G01860 @ ARAPORT AT1G01860.1 @ TAIR |
+1 | 9e-90 | 283 | 166/268 (62%) | Symbols: PFC1 | Ribosomal RNA adenine dimethylase family protein | chr1:304439-306275 REVERSE LENGTH=343 |
| BRACH PP3 | Bradi3g02232.3.p | +1 | 6e-141 | 415 | 244/266 (92%) | pacid=32819654 transcript=Bradi3g02232.3 locus=Bradi3g02232 ID=Bradi3g02232.3.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 (1953 bp)
>BART1_0-u42525.004 1953 150831_barley_pseudomolecules AAAAAAAAGATATCGCCTTCGAAAATGCTGGCGCTCACTTCCTTATCCCCGCGGCCTTCC CCGTCTCCGGCCACGCCTCCTCACCGCCGGCCGCCGCCGCCCCGCGGCCGTATCCGGCCC ACATCCGCCGTCGCAACGGCCGCATCCGACGGCGGCGGCGCGGGCGACGACTACCACTCG ACCATCCGCTCACTCAACTCGCACGGCCGCCGCCACGTCCCCCGCAAATCCCTCGGTCAG AACTACATGCTGAACGCGAGGGTGAACGAGGAGCTGGTGGCGGCGGCGGGGGTAGAGGTA GGGGACGTCGTGCTCGAGATAGGACCCGGGACGGGCTCGCTCACCGCCGCTCTGCTCGCC GCCGGCGCCACCGTCGTCGCCGTCGAGAAGGATAAGCATATGGCTACACTTGTGAGAGAT AGGTTTGGATCCACAGAGCAATTGAAGGTCATTGAAGAAGATATTACAAAATTTCACGTT CACTCCCATTTTCTCCCTATCCTGGACGAGAAATCCCGTGGCACGAAAAAATATGCCAAG GTTGTAGCAAACTTACCATTCAATGTCAGCACTGAAGTTGTCAAACAAATTCTCCCAATG GGAGATGTTTTCTCTGTCATGGTGCTCATGCTTCAGGATGAAGCAGCGCTACGCCTTGCA AATGCTTCAATACAAACACCAGAGTACCGACCTATCAATGTGTTTGTGAATTTCTACTCT GAACCCGAATACAAGTTCAAGGTAGAGAGGGCCAACTTTTTCCCTCAACCGACGGTTGAC GGTGGTGTTATAAGGTTTAAAATAAAGGATGCTGGGGAGTATCCGCCTGTTAGTTCTAAC AAAAGTTTTTTTTCAATGGTGAACTCCGCGTTCAATGGGAAGCGCAAGATGCTTCGGAAA TCACTTCAACACCTATATTCTTCTGTTGAAATCGAGGCCGCTCTTACCAATATCGGTCTT CCGCCTACAGTAAGCTCTCCCTCCATCCATCCATCCTTGCTCGTGCACTAAATTCATTAT TGCTGCAGGCTAGACCGTCGGAACTGATGATGGATGATTTCGTGAGGTTGCACAATCACC TGGGAAAAGTATGACCACCCCTGCATTCAAAATGCGTATGGAATCATCTTATTGGTTTGC TCGCTGGACTATGCATGCCTCTGAAGTGATTTTGTTCCCAGCTAGAGGGCACTGCAACTT GCAGATCATCCTTGCTGACAGTGACCGCCTAGTATTCTTCAGCAGTCCCACAGCCTTCAC CGCAACATAATTGGTGGCACAGCTTCAGCCCACGGTGTCCTTGCATGGATGATCATAGTG ATTGTGCTATAAGTTCAAAACCAATGATAATGCGCAGGGCATGATTTGCTCGCACAAGAA TTGCAGTTCTTTTCCTTATCGCAGATAGCATCCCTGCAAGAGGGAAGATACGCGGGCGTT GCATGTGTATAATTTACTGCAACTATCTATCCTCTTGTACTAATCTTCGCAGGTTGGAGG CAGAAATGTAGGGATCAAATGTCTGTCAGAACAATCTGAAGACCAGGCAAAGATGCTAGC TGCTCATAGTAAATTGCCAATAGCGTTTTTATGTGTGGACATAGATGGTAGATAGAGGTA CAGCCATTGCATTTTGAGCTTAAGTTTTGGCTATAAACTGCAACAAAAAGGTGCAAATGC TCAGTGTTTGAGTGAGCGATATTCTGCTGTTTTTTTACCTGGCAGCGTGTCGCTACGATG CAACATATAGTTAGTGGCAGTTCTTTTCCTGGCAAATACTTCCTCCGTCTAGAATTACTT GTCGCATAAATGAATAAAAATGAATGTACCTAGAACTAAAATACATCTAGCTACATCCAT TATTATGACAAGTATTTTCATACGAAGGGAATATCTGTTAACAAGCTGTGTTGTTATTTT ATTGGTAAACACTACTATTCATCTAATCGATTT
Protein Sequence (336 aa)
>BART1_0-u42525.004 336 150831_barley_pseudomolecules KKKISPSKMLALTSLSPRPSPSPATPPHRRPPPPRGRIRPTSAVATAASDGGGAGDDYHS TIRSLNSHGRRHVPRKSLGQNYMLNARVNEELVAAAGVEVGDVVLEIGPGTGSLTAALLA AGATVVAVEKDKHMATLVRDRFGSTEQLKVIEEDITKFHVHSHFLPILDEKSRGTKKYAK VVANLPFNVSTEVVKQILPMGDVFSVMVLMLQDEAALRLANASIQTPEYRPINVFVNFYS EPEYKFKVERANFFPQPTVDGGVIRFKIKDAGEYPPVSSNKSFFSMVNSAFNGKRKMLRK SLQHLYSSVEIEAALTNIGLPPTVSSPSIHPSLLVH