- Transcript BART1_0-u42525.007
- Transcript IDBART1_0-u42525.007
- Gene IDBART1_0-u42525
Barley RTD
Exon Structure of BART1_0-u42525.007
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22231287 | 22231191 | + |
| chr6H | 2 | 22231497 | 22231402 | + |
| chr6H | 3 | 22232507 | 22232423 | + |
| chr6H | 4 | 22233288 | 22233205 | + |
| chr6H | 5 | 22233733 | 22233388 | + |
| chr6H | 6 | 22234442 | 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 | 3.70105 | 1.60377 | 2.4174 |
| morex | ETI | 9.82793 | 1.4258 | 2.33038 |
| morex | LEA | 2.43627 | 1.02953 | 0.173946 |
| morex | EPI | 3.56975 | 4.58352 | 3.52903 |
| morex | ROO | 0.417662 | 0 | 0.0602167 |
| morex | ROO2 | 0 | 0.147651 | 0 |
| morex | NOD | 0.127498 | 0 | 0.591378 |
| morex | RAC | 0.641131 | 1.69342 | 0.880009 |
| morex | INF1 | 3.3292 | 2.11011 | 3.01627 |
| morex | INF2 | 2.35985 | 0.852587 | 3.1154 |
| morex | CAR5 | 1.17848 | 2.52309 | 1.03672 |
| morex | CAR15 | 0.0913216 | 0.274287 | 0.164215 |
| morex | LEM | 1.31129 | 0.478466 | 0.0227567 |
| morex | LOD | 0.439806 | 0.376283 | 0.242732 |
| morex | PAL | 1.78244 | 0.0000000076062 | 1.36527 |
| morex | SEN | 14.1431 | 5.59852 | 2.10689 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03050.2 | +2 | 2e-66 | 163 | 79/100 (79%) | protein|dimethyladenosine transferase, putative, expressed |
| TAIR PP10 | AT1G01860 @ ARAPORT AT1G01860.1 @ TAIR |
+2 | 8e-33 | 127 | 81/210 (39%) | Symbols: PFC1 | Ribosomal RNA adenine dimethylase family protein | chr1:304439-306275 REVERSE LENGTH=343 |
| BRACH PP3 | Bradi3g02232.3.p | +2 | 3e-59 | 198 | 122/207 (59%) | pacid=32819654 transcript=Bradi3g02232.3 locus=Bradi3g02232 ID=Bradi3g02232.3.v3.1 annot-version=v3.1 |
Barley PseudoMolecules GBrowse
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grey: non-coding, green: Barley Morex IBSC 2017 Transcript CDS, red: Barley RTD exons
CDS Sequence (1326 bp)
>BART1_0-u42525.007 1326 150831_barley_pseudomolecules GCAGGTCATTGAAGAAGATATTACAAAATTTCACGTTCACTCCCATTTTCTCCCTATCCT GGACGAGAAATCCCGTGGCACGAAAAAATATGCCAAGGTTGTAGCAAACTTACCATTCAA TGTCAGCACTGAAGTTGTCAAACAAATTCTCCCAATGGGAGATGTTTTCTCTGTCATGGT GCTCATGCTTCAGGATGAAGCAGCGCTACGCCTTGCAAATGCTTCAATACAAACACCAGA GTACCGACCTATCAATGTGTTTGTGAATTTCTACTCTGGTTGACGGTGGTGTTATAAGGT TTAAAATAAAGGATGCTGGGGAGTATCCGCCTGTTAGTTCTAACAAAAGTTTTTTTTCAA TGGTGAACTCCGCGTTCAATGGGAAGCGCAAGATGCTTCGGAAATCACTTCAACACCTAT ATTCTTCTGTTGAAATCGAGGCCGCTCTTACCAATATCGGTCTTCCGCCTACAGTAAGCT CTCCCTCCATCCATCCATCCTTGCTCGTGCACTAAATTCATTATTGCTGCAGGCTAGACC GTCGGAACTGATGATGGATGATTTCGTGAGGTTGCACAATCACCTGGGAAAAGTATGACC ACCCCTGCATTCAAAATGCGTATGGAATCATCTTATTGGTTTGCTCGCTGGACTATGCAT GCCTCTGAAGTGATTTTGTTCCCAGCTAGAGGGCACTGCAACTTGCAGATCATCCTTGCT GACAGTGACCGCCTAGTATTCTTCAGCAGTCCCACAGCCTTCACCGCAACATAATTGGTG GCACAGCTTCAGCCCACGGTGTCCTTGCATGGATGATCATAGTGATTGTGCTATAAGTTC AAAACCAATGATAATGCGCAGGGCATGATTTGCTCGCACAAGAATTGCAGTTCTTTTCCT TATCGCAGATAGCATCCCTGCAAGAGGGAAGATACGCGGGCGTTGCATGTGTATAATTTA CTGCAACTATCTATCCTCTTGTACTAATCTTCGCAGGTTGGAGGCAGAAATGTAGGGATC AAATGTCTGTCAGAACAATCTGAAGACCAGGCAAAGATGCTAGCTGCTCATAGTAAATTG CCAATAGCGTTTTTATGTGTGGACATAGATGGTAGATAGAGGTACAGCCATTGCATTTTG AGCTTAAGTTTTGGCTATAAACTGCAACAAAAAGGTGCAAATGCTCAGTGTTTGAGTGAG CGATATTCTGCTGTTTTTTTACCTGGCAGCGTGTCGCTACGATGCAACATATAGTTAGTG GCAGTTCTTTTCCTGGCAAATACTTCCTCCGTCTAGAATTACTTGTCGCATAAATGAATA AAAATG
Protein Sequence ( aa)
>BART1_0-u42525.007 150831_barley_pseudomolecules