- Transcript BART1_0-u53404.013
- Transcript IDBART1_0-u53404.013
- Gene IDBART1_0-u53404
Barley RTD
Exon Structure of BART1_0-u53404.013
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr7H | 1 | 387995344 | 387994911 | - |
| chr7H | 2 | 387996154 | 387996027 | - |
| chr7H | 3 | 387996488 | 387996230 | - |
| chr7H | 4 | 387996656 | 387996577 | - |
| chr7H | 5 | 387996872 | 387996751 | - |
| chr7H | 6 | 387997091 | 387997001 | - |
| chr7H | 7 | 387997326 | 387997189 | - |
| chr7H | 8 | 387997561 | 387997429 | - |
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 | 0.885165 | 0.334932 | 0.600387 |
| morex | LEA | 0 | 0 | 0 |
| morex | EPI | 0 | 0.397702 | 0.511789 |
| morex | ROO | 0 | 0 | 0 |
| morex | ROO2 | 0.383412 | 0 | 0 |
| morex | NOD | 0 | 0.701743 | 0 |
| morex | RAC | 0 | 0.175426 | 0.378494 |
| morex | INF1 | 0 | 0 | 0 |
| morex | INF2 | 0.313502 | 0.279212 | 0 |
| morex | CAR5 | 0 | 0 | 0 |
| morex | CAR15 | 0.129783 | 0 | 0 |
| morex | LEM | 0 | 0.159465 | 0.1547 |
| morex | LOD | 0 | 0.189241 | 0 |
| morex | PAL | 0 | 0 | 0 |
| morex | SEN | 0.378608 | 0 | 0 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os08g06050.1 | +1 | 1e-144 | 219 | 102/113 (90%) | protein|OsTOP6A2 - Topoisomerase 6 subunit A homolog 2, expressed |
| TAIR PP10 | AT1G63990 @ ARAPORT AT1G63990.1 @ TAIR |
+1 | 3e-109 | 179 | 81/112 (72%) | Symbols: SPO11-2 | sporulation 11-2 | chr1:23743323-23745351 REVERSE LENGTH=383 |
| BRACH PP3 | Bradi3g16580.1.p | +1 | 2e-156 | 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 (1385 bp)
>BART1_0-u53404.013 1385 150831_barley_pseudomolecules CAGATTTCCCGCAAGTCCACCAACTGCAGCCTGCGCAGCGGCTTGCTGAGTGATGTTTCA TCGGTGTATCTGTCCTACGCCTTCTGCAAGAGGTCGCTAATGAGAGAAAATGATGCCAAG GCATTCGTCAGAGTATGGAAAGTCATGGAGATGTGCTACAAGATCTTGGGCGAAGGGAAG CTTGTCACCCAGCGGGAGTTGTTCTACAAACTACTGTCGGACTCACCCAAGTACTTCAGC TGTCAGCGTCATGTGAATCAAACCATCCAAGATGTTGTTTCATTGCTCCGTTGCACAAGG CAGAGTTTAGGAATCATGGCATCAAGTAGAGGGGCACTGATTGGACGACTTGTGTTGCAT GTAGGAAGAACACATCGATTGTTCCATTCTCGGACCTTCTGGGCATGCCATTACTGGGGA TCTGAACCAATTGAGCAGATTAAATTTGTCTTCAGATGCCCGTTATCTCATTCTAGTGGA GAAGAGGCTGGCTGAAGACCGCTTATATAATCAGCTTCCATGTATCCTGATCACTGCAAA AGGATATCCTGATATCGCAACGAGGTTTATCTTGCATCGACTGAGCCAGACTTTTCCAAA TATGCCAATATTTGCATTAGTGGACTGGTTAAGCCCTTTCTAATGTTTTTCTTTTTTGAG AACGGAAGCACTTTCTAATGTTAATACTATGTGTACTATTTTGGTTGTTTGTTTTCTGGA TAAAGTTAGATTCCTTCCCAATTCAGGAACCCTGCAGGGCTCTCTATACTGTGTACTTAC AAATATGGAAGCATATCAATGGGCTTGGAATCATACAGATACGCTTGCAATGTAAAATGG CTTGGCCTAAGAGGAGATGATCTGCAGCTTATCCCTCAGAGTTCATTCCAAGAGTTGAAA CCTCGTGATTTGCAGGTCGCCAAAAGCTTGCTGTCATCTAAGTTTCTTCAGGACACGCAC AGAGCGGAGTTGACACGGATGGTCGAGACGGGCACGCGTGCTGAGATCGAAGCTCTCTAT TGCCATGGTTTTGATTTCCTGGGGAAGTTCATCGCCAGGAAGATTGTGCAGGGTGATTAC ATTTGACAGTGTTTTTTCTCTCTGGCTGTATGGCTCATGATGACGAGGCTACTGGTACAG TAGTGTGAGTGTCTCTGTTAATTGGAGAGCGATATCGCCCATGGCTCATTATGGCTGGTG AGGTCTGAACTTTGACATGCATAGAACAAAACGGATAGTAAAAGTTCTCCCTCTGAGAGT GGAACGATAGCAAGTAAGCACGGTTGTACTCCAGTATATTCGTTTAGGCGGTCAGGGTAA TTCAGTTTCTGGTGTATGCGTATGCCTTCTGCGCTCCCTGACAGTACTCTCCCCATAAAA TTGGC
Protein Sequence (164 aa)
>BART1_0-u53404.013 164 150831_barley_pseudomolecules QISRKSTNCSLRSGLLSDVSSVYLSYAFCKRSLMRENDAKAFVRVWKVMEMCYKILGEGK LVTQRELFYKLLSDSPKYFSCQRHVNQTIQDVVSLLRCTRQSLGIMASSRGALIGRLVLH VGRTHRLFHSRTFWACHYWGSEPIEQIKFVFRCPLSHSSGEEAG