- Transcript BART1_0-u42525.005
- Transcript IDBART1_0-u42525.005
- Gene IDBART1_0-u42525
Barley RTD
Exon Structure of BART1_0-u42525.005
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22229404 | 22229189 | + |
| 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 | 22233498 | 22233388 | + |
| chr6H | 10 | 22233733 | 22233596 | + |
| chr6H | 11 | 22234390 | 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 | 0.850073 | 0 |
| morex | ETI | 0 | 0 | 0 |
| morex | LEA | 0 | 0.788057 | 0 |
| morex | EPI | 0 | 0 | 0.680645 |
| morex | ROO | 0 | 0.205576 | 0 |
| morex | ROO2 | 0.155848 | 0 | 0 |
| morex | NOD | 0 | 0 | 0 |
| morex | RAC | 1.10606 | 0 | 0.214773 |
| morex | INF1 | 0 | 0 | 0.834598 |
| morex | INF2 | 0 | 0 | 0 |
| morex | CAR5 | 0 | 0 | 0 |
| morex | CAR15 | 0.198027 | 0 | 0 |
| morex | LEM | 0.820509 | 0 | 0.00215241 |
| morex | LOD | 0 | 0.0063236 | 0 |
| morex | PAL | 0 | 0.0000000614604 | 0.614118 |
| morex | SEN | 1.42203 | 0 | 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 | 3e-110 | 328 | 159/190 (84%) | protein|dimethyladenosine transferase, putative, expressed |
| TAIR PP10 | AT1G01860 @ ARAPORT AT1G01860.1 @ TAIR |
+1 | 7e-79 | 251 | 149/245 (61%) | Symbols: PFC1 | Ribosomal RNA adenine dimethylase family protein | chr1:304439-306275 REVERSE LENGTH=343 |
| BRACH PP3 | Bradi3g02232.3.p | +1 | 9e-126 | 372 | 223/243 (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 (1649 bp)
>BART1_0-u42525.005 1649 150831_barley_pseudomolecules CGAAAATGCTGGCGCTCACTTCCTTATCCCCGCGGCCTTCCCCGTCTCCGGCCACGCCTC CTCACCGCCGGCCGCCGCCGCCCCGCGGCCGTATCCGGCCCACATCCGCCGTCGCAACGG CCGCATCCGACGGCGGCGGCGCGGGCGACGACTACCACTCGACCATCCGCTCACTCAACT CGCACGGCCGCCGCCACGTCCCCCGCAAATCCCTCGAACTACATGCTGAACGCGAGGGTG AACGAGGAGCTGGTGGCGGCGGCGGGGGTAGAGGTAGGGGACGTCGTGCTCGAGATAGGA CCCGGGACGGGCTCGCTCACCGCCGCTCTGCTCGCCGCCGGCGCCACCGTCGTCGCCGTC GAGAAGGATAAGCATATGGCTACACTTGTGAGAGATAGGTTTGGATCCACAGAGCAATTG AAGGTCATTGAAGAAGATATTACAAAATTTCACGTTCACTCCCATTTTCTCCCTATCCTG GACGAGAAATCCCGTGGCACGAAAAAATATGCCAAGGTTGTAGCAAACTTACCATTCAAT GTCAGCACTGAAGTTGTCAAACAAATTCTCCCAATGGGAGATGTTTTCTCTGTCATGGTG CTCATGCTTCAGGATGAAGCAGCGCTACGCCTTGCAAATGCTTCAATACAAACACCAGAG TACCGACCTATCAATGTGTTTGTGAATTTCTACTCTGAACCCGAATACAAGTTCAAGGTA GAGAGGGCCAACTTTTTCCCTCAACCGACGGTTGACGGTGGTGTTATAAGGTTTAAAATA AAGGATGCTGGGGAGTATCCGCCTGTTAGTTCTAACAAAAGTTTTTTTTCAATGGTGAAC TCCGCGTTCAATGGGAAGCGCAAGATGCTTCGGAAATCACTTCAACACCTATATTCTTCT GTTGAAATCGAGGCCGCTCTTACCAATATCGGTCTTCCGCCTACAGTTGCACAATCACCT GGGAAAAGTATGACCACCCCTGCATTCAAAATGCGTATGGAATCATCTTATTGGTTTGCT CGCTGGACTATGCATGCCTCTGAAGTGATTTTGTTCCCAGCTAGAGGGCACTGCAACTTG CAGATCATCCTTGCTGACAGTGACCGCCTAGTATTCTTCAGCAGTCCCACAGCCTTCACC GCAACATAATTGGTGGCACAGCTTCAGCCCACGGTGTCCTTGCATGGATGATCATAGTGA TTGTGCTATAAGTTCAAAACCAATGATAATGCGCAGGGCATGATTTGCTCGCACAAGAAT TGCAGTTCTTTTCCTTATCGCAGATAGCATCCCTGCAAGAGGGAAGATACGCGGGCGTTG CATGTGTATAATTTACTGCAACTATCTATCCTCTTGTACTAATCTTCGCAGGTTGGAGGC AGAAATGTAGGGATCAAATGTCTGTCAGAACAATCTGAAGACCAGGCAAAGATGCTAGCT GCTCATAGTAAATTGCCAATAGCGTTTTTATGTGTGGACATAGATGGTAGATAGAGGTAC AGCCATTGCATTTTGAGCTTAAGTTTTGGCTATAAACTGCAACAAAAAGGTGCAAATGCT CAGTGTTTGAGTGAGCGATATTCTGCTGTTTTTTTACCTGGCAGCGTGTCGCTACGATGC AACATATAGTTAGTGGCAGTTCTTTTCCT
Protein Sequence (382 aa)
>BART1_0-u42525.005 382 150831_barley_pseudomolecules RKCWRSLPYPRGLPRLRPRLLTAGRRRPAAVSGPHPPSQRPHPTAAARATTTTRPSAHST RTAAATSPANPSNYMLNARVNEELVAAAGVEVGDVVLEIGPGTGSLTAALLAAGATVVAV EKDKHMATLVRDRFGSTEQLKVIEEDITKFHVHSHFLPILDEKSRGTKKYAKVVANLPFN VSTEVVKQILPMGDVFSVMVLMLQDEAALRLANASIQTPEYRPINVFVNFYSEPEYKFKV ERANFFPQPTVDGGVIRFKIKDAGEYPPVSSNKSFFSMVNSAFNGKRKMLRKSLQHLYSS VEIEAALTNIGLPPTVAQSPGKSMTTPAFKMRMESSYWFARWTMHASEVILFPARGHCNL QIILADSDRLVFFSSPTAFTAT