- Transcript BART1_0-u53404.012
- Transcript IDBART1_0-u53404.012
- Gene IDBART1_0-u53404
Barley RTD
Exon Structure of BART1_0-u53404.012
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr7H | 1 | 387995344 | 387994903 | - |
| chr7H | 2 | 387996154 | 387996027 | - |
| chr7H | 3 | 387996488 | 387996230 | - |
| chr7H | 4 | 387996656 | 387996577 | - |
| chr7H | 5 | 387996879 | 387996751 | - |
| chr7H | 6 | 387997326 | 387997189 | - |
| chr7H | 7 | 387997558 | 387997429 | - |
| chr7H | 8 | 387998187 | 387997921 | - |
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 | 1.05553 | 2.25348 | 0.912564 |
| morex | ETI | 3.64181 | 1.85717 | 1.93297 |
| morex | LEA | 1.57778 | 0.613814 | 0.306153 |
| morex | EPI | 1.60842 | 5.58416 | 2.22067 |
| morex | ROO | 0.583684 | 0.476242 | 0.323595 |
| morex | ROO2 | 1.19202 | 1.43938 | 0.552879 |
| morex | NOD | 1.18672 | 1.63355 | 5.28795 |
| morex | RAC | 2.11535 | 1.82908 | 1.55531 |
| morex | INF1 | 1.48366 | 1.62063 | 2.14036 |
| morex | INF2 | 4.1701 | 3.93546 | 2.92622 |
| morex | CAR5 | 3.90598 | 1.71879 | 4.3849 |
| morex | CAR15 | 1.56862 | 0.619598 | 0.947318 |
| morex | LEM | 1.32448 | 1.49645 | 1.17114 |
| morex | LOD | 1.32887 | 1.51936 | 0.772518 |
| morex | PAL | 1.30551 | 1.26656 | 1.55501 |
| morex | SEN | 2.19876 | 1.69761 | 1.01936 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os08g06050.1 | +1 | 3e-136 | 219 | 102/113 (90%) | protein|OsTOP6A2 - Topoisomerase 6 subunit A homolog 2, expressed |
| TAIR PP10 | AT1G63990 @ ARAPORT AT1G63990.1 @ TAIR |
+1 | 4e-100 | 179 | 81/112 (72%) | Symbols: SPO11-2 | sporulation 11-2 | chr1:23743323-23745351 REVERSE LENGTH=383 |
| BRACH PP3 | Bradi3g16580.1.p | +1 | 3e-147 | 216 | 100/113 (88%) | pacid=32817968 transcript=Bradi3g16580.1 locus=Bradi3g16580 ID=Bradi3g16580.1.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 (1573 bp)
>BART1_0-u53404.012 1573 150831_barley_pseudomolecules CGGAGGCGGAGGCGGAGGCGGAGGTTCCCGCAGCGTCGCTCTTCGGTGCGGACTGCCGCC TCTGCTCAGCCGACGTGCTCTCGCCCCCCGAGGTCTGTCATACGCCAACTTCCCTCGTCC GCCTCTGCCTCTGATCGAATCGACATGCTTTGCTTCTATTGTGTGTGGCCAACTCGATAG GTTCGGGCAAGGATCGAGGTGGCGGTGCTCAATTTCCTCGCCTTGCTTTCGTCTCCCTCT TCTCCGTCCATCTCCGTCCTCCCCCTGATTTCCCGCAAGTCCACCAACTGCAGCCTGCGC AGCGGCTTGCTGAGTGATGTTTCATCGGTGTATCTGTCCTACGCCTTCTGCAAGAGGTCG CTAATGAGAGAAAATGATGCCAAGGCATTCGTCAGAGTATGGAAAGTCATGGAGATGTGC TACAAGATCTTGGGCGAAGGGAAGCTTGTCACCCAGCGGGAGTTGTTCTACAAACTACTG TCGGACTCACCCAAGTACTTCAGCTGTCAGCGTCATGTGAATCAAACCATCCAAGGAACC AGAGGAAGAACACATCGATTGTTCCATTCTCGGACCTTCTGGGCATGCCATTACTGGGGA TCTGAACCAATTGAGCAGATTAAATTTGTCTTCAGATGCCCGTTATCTCATTCTAGTGGA GAAGAGGCTGGCTGAAGACCGCTTATATAATCAGCTTCCATGTATCCTGATCACTGCAAA AGGATATCCTGATATCGCAACGAGGTTTATCTTGCATCGACTGAGCCAGACTTTTCCAAA TATGCCAATATTTGCATTAGTGGACTGGTTAAGCCCTTTCTAATGTTTTTCTTTTTTGAG AACGGAAGCACTTTCTAATGTTAATACTATGTGTACTATTTTGGTTGTTTGTTTTCTGGA TAAAGTTAGATTCCTTCCCAATTCAGGAACCCTGCAGGGCTCTCTATACTGTGTACTTAC AAATATGGAAGCATATCAATGGGCTTGGAATCATACAGATACGCTTGCAATGTAAAATGG CTTGGCCTAAGAGGAGATGATCTGCAGCTTATCCCTCAGAGTTCATTCCAAGAGTTGAAA CCTCGTGATTTGCAGGTCGCCAAAAGCTTGCTGTCATCTAAGTTTCTTCAGGACACGCAC AGAGCGGAGTTGACACGGATGGTCGAGACGGGCACGCGTGCTGAGATCGAAGCTCTCTAT TGCCATGGTTTTGATTTCCTGGGGAAGTTCATCGCCAGGAAGATTGTGCAGGGTGATTAC ATTTGACAGTGTTTTTTCTCTCTGGCTGTATGGCTCATGATGACGAGGCTACTGGTACAG TAGTGTGAGTGTCTCTGTTAATTGGAGAGCGATATCGCCCATGGCTCATTATGGCTGGTG AGGTCTGAACTTTGACATGCATAGAACAAAACGGATAGTAAAAGTTCTCCCTCTGAGAGT GGAACGATAGCAAGTAAGCACGGTTGTACTCCAGTATATTCGTTTAGGCGGTCAGGGTAA TTCAGTTTCTGGTGTATGCGTATGCCTTCTGCGCTCCCTGACAGTACTCTCCCCATAAAA TTGGCAATCCAAA
Protein Sequence (103 aa)
>BART1_0-u53404.012 103 150831_barley_pseudomolecules MRENDAKAFVRVWKVMEMCYKILGEGKLVTQRELFYKLLSDSPKYFSCQRHVNQTIQGTR GRTHRLFHSRTFWACHYWGSEPIEQIKFVFRCPLSHSSGEEAG