- Transcript BART1_0-u53404.011
- Transcript IDBART1_0-u53404.011
- Gene IDBART1_0-u53404
Barley RTD
Exon Structure of BART1_0-u53404.011
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr7H | 1 | 387995344 | 387994893 | - |
| chr7H | 2 | 387996154 | 387996027 | - |
| chr7H | 3 | 387996488 | 387996230 | - |
| chr7H | 4 | 387996671 | 387996577 | - |
| chr7H | 5 | 387996879 | 387996751 | - |
| chr7H | 6 | 387997091 | 387997003 | - |
| chr7H | 7 | 387997326 | 387997189 | - |
| chr7H | 8 | 387997558 | 387997429 | - |
| chr7H | 9 | 387998234 | 387998096 | - |
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 | 2.98017 | 1.3573 | 5.507 |
| morex | ETI | 14.3146 | 15.2841 | 15.7381 |
| morex | LEA | 5.931 | 4.19694 | 8.00739 |
| morex | EPI | 9.56515 | 7.68753 | 12.8756 |
| morex | ROO | 1.54444 | 3.40069 | 1.23628 |
| morex | ROO2 | 3.00484 | 2.28026 | 3.54775 |
| morex | NOD | 2.16731 | 5.08234 | 3.4771 |
| morex | RAC | 6.21219 | 6.97381 | 6.45933 |
| morex | INF1 | 3.81984 | 4.12581 | 3.98912 |
| morex | INF2 | 4.47842 | 5.24961 | 7.1791 |
| morex | CAR5 | 8.85844 | 8.73121 | 5.70172 |
| morex | CAR15 | 0.881627 | 1.60608 | 0.625161 |
| morex | LEM | 6.70148 | 6.02465 | 4.89028 |
| morex | LOD | 7.4477 | 6.18879 | 5.74811 |
| morex | PAL | 4.03595 | 4.73615 | 4.80469 |
| morex | SEN | 6.72144 | 5.53866 | 8.88547 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os08g06050.1 | +2 | 3e-161 | 370 | 198/264 (75%) | protein|OsTOP6A2 - Topoisomerase 6 subunit A homolog 2, expressed |
| TAIR PP10 | AT1G63990 @ ARAPORT AT1G63990.1 @ TAIR |
+2 | 3e-119 | 269 | 136/215 (63%) | Symbols: SPO11-2 | sporulation 11-2 | chr1:23743323-23745351 REVERSE LENGTH=383 |
| BRACH PP3 | Bradi3g16580.1.p | +2 | 4e-175 | 418 | 222/263 (84%) | pacid=32817968 transcript=Bradi3g16580.1 locus=Bradi3g16580 ID=Bradi3g16580.1.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 (1559 bp)
>BART1_0-u53404.011 1559 150831_barley_pseudomolecules ATCGTCCTCCGATGTAGGAAGTGCAGCGCGGATGGCGATGGCGGAGGCGGAGGCGGAGGC GGAGGCGGAGGTTCCCGCAGCGTCGCTCTTCGGTGCGGACTGCCGCCTCTGCTCAGCCGA CGTGCTCTCGCCCCCCGAGATTTCCCGCAAGTCCACCAACTGCAGCCTGCGCAGCGGCTT GCTGAGTGATGTTTCATCGGTGTATCTGTCCTACGCCTTCTGCAAGAGGTCGCTAATGAG AGAAAATGATGCCAAGGCATTCGTCAGAGTATGGAAAGTCATGGAGATGTGCTACAAGAT CTTGGGCGAAGGGAAGCTTGTCACCCAGCGGGAGTTGTTCTACAAACTACTGTCGGACTC ACCCAAGTACTTCAGCTGTCAGCGTCATGTGAATCAAACCATCCAAGATGTTGTTTCATT GCTCCGTTGCACAAGGCAGAGTTTAGGAATCATGGCATCAAGTAGAGGGGCACTGATTGG ACGACTTGTGTTGCATGAACCAGAGGAAGAACACATCGATTGTTCCATTCTCGGACCTTC TGGGCATGCCATTACTGGGGATCTGAACCAATTGAGCAGATTAAATTTGTCTTCAGATGC CCGTTATCTCATTCTAGTGGAGAAGGATGCCATATTTCAGAGGCTGGCTGAAGACCGCTT ATATAATCAGCTTCCATGTATCCTGATCACTGCAAAAGGATATCCTGATATCGCAACGAG GTTTATCTTGCATCGACTGAGCCAGACTTTTCCAAATATGCCAATATTTGCATTAGTGGA CTGGTTAAGCCCTTTCTAATGTTTTTCTTTTTTGAGAACGGAAGCACTTTCTAATGTTAA TACTATGTGTACTATTTTGGTTGTTTGTTTTCTGGATAAAGTTAGATTCCTTCCCAATTC AGGAACCCTGCAGGGCTCTCTATACTGTGTACTTACAAATATGGAAGCATATCAATGGGC TTGGAATCATACAGATACGCTTGCAATGTAAAATGGCTTGGCCTAAGAGGAGATGATCTG CAGCTTATCCCTCAGAGTTCATTCCAAGAGTTGAAACCTCGTGATTTGCAGGTCGCCAAA AGCTTGCTGTCATCTAAGTTTCTTCAGGACACGCACAGAGCGGAGTTGACACGGATGGTC GAGACGGGCACGCGTGCTGAGATCGAAGCTCTCTATTGCCATGGTTTTGATTTCCTGGGG AAGTTCATCGCCAGGAAGATTGTGCAGGGTGATTACATTTGACAGTGTTTTTTCTCTCTG GCTGTATGGCTCATGATGACGAGGCTACTGGTACAGTAGTGTGAGTGTCTCTGTTAATTG GAGAGCGATATCGCCCATGGCTCATTATGGCTGGTGAGGTCTGAACTTTGACATGCATAG AACAAAACGGATAGTAAAAGTTCTCCCTCTGAGAGTGGAACGATAGCAAGTAAGCACGGT TGTACTCCAGTATATTCGTTTAGGCGGTCAGGGTAATTCAGTTTCTGGTGTATGCGTATG CCTTCTGCGCTCCCTGACAGTACTCTCCCCATAAAATTGGCAATCCAAATGTTGCAGGC
Protein Sequence (253 aa)
>BART1_0-u53404.011 253 150831_barley_pseudomolecules MAEAEAEAEAEVPAASLFGADCRLCSADVLSPPEISRKSTNCSLRSGLLSDVSSVYLSYA FCKRSLMRENDAKAFVRVWKVMEMCYKILGEGKLVTQRELFYKLLSDSPKYFSCQRHVNQ TIQDVVSLLRCTRQSLGIMASSRGALIGRLVLHEPEEEHIDCSILGPSGHAITGDLNQLS RLNLSSDARYLILVEKDAIFQRLAEDRLYNQLPCILITAKGYPDIATRFILHRLSQTFPN MPIFALVDWLSPF