- Transcript BART1_0-u34851.003
- Transcript IDBART1_0-u34851.003
- Gene IDBART1_0-u34851
Barley RTD
Exon Structure of BART1_0-u34851.003
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 280032389 | 280031114 | + |
| chr5H | 2 | 280032568 | 280032468 | + |
| chr5H | 3 | 280032882 | 280032720 | + |
| chr5H | 4 | 280033483 | 280033320 | + |
| chr5H | 5 | 280034038 | 280033780 | + |
| chr5H | 6 | 280034628 | 280034140 | + |
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 | 3.21946 | 3.9862 | 5.53819 |
| morex | LEA | 2.10444 | 3.32977 | 1.72745 |
| morex | EPI | 30.1573 | 12.2217 | 29.8658 |
| morex | ROO | 0 | 0 | 0 |
| morex | ROO2 | 0 | 0 | 0.0488099 |
| morex | NOD | 0 | 0 | 0 |
| morex | RAC | 3.86778 | 2.70828 | 2.92169 |
| morex | INF1 | 0.0663446 | 0 | 0.090235 |
| morex | INF2 | 1.21902 | 1.23355 | 0 |
| morex | CAR5 | 0 | 0.71965 | 0.486325 |
| morex | CAR15 | 2.78283 | 2.38446 | 3.62582 |
| morex | LEM | 0 | 0 | 5.06457 |
| morex | LOD | 0.338213 | 0.186491 | 0 |
| morex | PAL | 2.28602 | 3.71758 | 2.89882 |
| morex | SEN | 8.36776 | 4.10738 | 3.9224 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os12g31000.1 | +2 | 0.0 | 586 | 332/523 (63%) | protein|pumilio-family RNA binding repeat domain containing protein, expressed |
| TAIR PP10 | AT1G22240 @ ARAPORT AT1G22240.1 @ TAIR |
+2 | 2e-101 | 323 | 161/319 (50%) | Symbols: APUM8, PUM8 | pumilio 8 | chr1:7853084-7854963 FORWARD LENGTH=515 |
| BRACH PP3 | Bradi4g07100.1.p | +2 | 0.0 | 717 | 386/507 (76%) | pacid=32788499 transcript=Bradi4g07100.1 locus=Bradi4g07100 ID=Bradi4g07100.1.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 (2452 bp)
>BART1_0-u34851.003 2452 150831_barley_pseudomolecules GGATAGATAGCCCAACCAACGCCTGCCCATCCTTCCCCTCCATTTGCAAATTTGGATCTT GTTCCATTCCAACAAATATCCTGCGCATGGGGAGATATTTTCTTTGCGCTGGCCAGGGTC ACTCACAAGTGGGTCCCAAAGTGCACCGGATGTCTGCCTCTAGAGACCCAACAAAAGCGT ATTTTAAGGGAGGGAAGAGGTCACTGGACGAGAGTGGGCCAAGTCATATGTGTGTGCAGC CAGAAATAGGTGTTTGTGAACCACCGAAGATATTTGGGCTGAGATATTATCTATTTTTGT ATTTCCTTTTTTGTTTTCATTTTCGGAGTTGTAGTAGTAATAGAAATGTTTTTTAAGGGT CTAAATATCTGATGTTGAAATAAAAAGTCGGAAAGTGCTTACCCCAAAACAAGAAAATCA GACCAGGTAATAACCTTTCAAAAGAAAAGATTTAAAAGAAGAAGAAAAAAAGCACTCCTC TCACCGGCATCAGTCCTCACTACTTTCGCGCTATCCTTATATAAAAGCACCCCCTCTGCT CTCTCCTCCTCCCACTCCTGCATGCCTCAACGAACCATCTCCAGGAAAACACCTCACCCC AATCCAACCCCAAACCAATCCTCTCCACAAACAAATCTAACAGAATTCCCCCACTGATTT TCTCATCGAGATTCGATCAAGATAGTAGTTGGAGATGAAGCTGGACAGGGAGATGGAGAT GCTCCTCAACGAGATCCCTCTCCTCCTCCACGGCGACGTCCTCGGCTGCAGCGAGCCAGC CGCCGCCGAGACCGACGCCGGCGCCGTCGACTTCGCTTATCTCATCCAAGAACTCGGCGA GATGGGGTTCGTCGAGGACGACGACGACGACGACAGTTTCCTTTACCCAAGGAAGGCCAG CTCATCTCCGACGAGCAACCTCCATTTCATGGACGCTGAGAATTTCGTGGCGTCGCATCC CTTCTCCATGGACAAAGACCGCGAGAGGGCTCTTTTCGATCCGTTTCCCTTCTCCAGCAC CTGCTTCGACGCCGCCGTGGGCGACGACTGGGACCTCCTGTGTCGGCCGGTGAGGTCCCG GCTGTGCAAGACGGCGAGGCCGAAGAAGGGTACCTGCAGCAACGGCTGCCAGGCGACGAG CCCCAAGAAGTGCGCGGCGGCGAAGCCGTCCAAGTACGAGAGCCTTGTCGGGCTGCGCGG GTACATGTACCACGTGGCCAGGGACCAGCACGGCTGCCGGTTCCTCCAGCAGCGGCTCGA CGACGGCAAGCGCGAGAAGCTGCTAGCCGTCTGCAGCGAGGAGCAGAGGATGGGCATCGT GCTGACCCTCACAAAGGAACCCTTCGTGCTCGTCAGGATCTCTCTCAATGTACATGGGAC AAGGGCGGTTCAGAAGCTGATTGAAAGCTTGAAGGCAAGGGAGGAGATTCAGCTCGTCGT CGCAGCTCTGCGCCCCGGGTTCCTGGAGCTCATAAAGGATCCTAATGGTAATCATGTCGT GCAGAAGTGCTTGCAATCGTTCGGGGCCGATGATAACAAGCCGATCTTCGATGCTGCTGC TATTTACTGCCTTGATATTGGGATGCAATGCCATGGCTGCTGCGTCCTACAGCGGTGTAT CGCGCGTTCGACTGGTGAGCACAAGGAGAAGCTGGTTGCCGCGATCGCTCGCAATGGGTT CGAACTTGCACAGGATGCCTATGGAAACTATGTTGTTCAGTATGTGATAGAACTAAAGGT CGCTGCTGCAAATGCAAGTCTGGCACAACAGTTTGAAGGCAAGTACATCCACCTCTCCAT GCAGAAGTTCAGCAGCAACGTTGTCGAGAAATGCCTGAAAGTTTTCAAGGAAGCTGACAA AGCGAACATCATCCTGCAGCTCCTTGCTGCGCCGCAGTTCGAGCGGTTGCTTCTGCACCC TTACGCAAACTATGTAGTCTACGCAGCACTTCAGAATTCCAAGGGCTCTCTACACTCTGC ACTGACCAACGCGATCCGGCCTCACGTGGAGCTACTCAGGACCAGCCCATACTGCAAGAG GATCTACTCTCGAGCTTTGCTGAAAAAGTGATGGTCTGATGAGACCATCTCACCATGTGT AACAATAAAGATAGTTTGTCTTGTGCTATTTTTTCGGATTCAAAAGGGATAAAAGTGATC TCACCATGTAGATCTTGTATAGATCAAAATTTATTTGGTCATGTACTTCTATGTGCACCT TTATTTGATGCACTCTTCCGTTGCCATAATCCATCTGGAATGGTAAGTTCCGATCTAACA AATCGTCATATAGATGTTGATGCACGTACACAATATTGGTGATGTTTCTTGTAACTTAAT GTTTGCATTTTTTTTTGCCCTGCAATTGCTCAACCGAATGCCAAAACATGAAGGCAAATA ACTGATTTGCAGTCTAAGGAAAGTTACGTGTGACTTTTTCGTAATACATCAC
Protein Sequence (458 aa)
>BART1_0-u34851.003 458 150831_barley_pseudomolecules MKLDREMEMLLNEIPLLLHGDVLGCSEPAAAETDAGAVDFAYLIQELGEMGFVEDDDDDD SFLYPRKASSSPTSNLHFMDAENFVASHPFSMDKDRERALFDPFPFSSTCFDAAVGDDWD LLCRPVRSRLCKTARPKKGTCSNGCQATSPKKCAAAKPSKYESLVGLRGYMYHVARDQHG CRFLQQRLDDGKREKLLAVCSEEQRMGIVLTLTKEPFVLVRISLNVHGTRAVQKLIESLK AREEIQLVVAALRPGFLELIKDPNGNHVVQKCLQSFGADDNKPIFDAAAIYCLDIGMQCH GCCVLQRCIARSTGEHKEKLVAAIARNGFELAQDAYGNYVVQYVIELKVAAANASLAQQF EGKYIHLSMQKFSSNVVEKCLKVFKEADKANIILQLLAAPQFERLLLHPYANYVVYAALQ NSKGSLHSALTNAIRPHVELLRTSPYCKRIYSRALLKK