- Transcript BART1_0-u42531.004
- Transcript IDBART1_0-u42531.004
- Gene IDBART1_0-u42531
Barley RTD
Exon Structure of BART1_0-u42531.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22237035 | 22236577 | + |
| chr6H | 2 | 22237825 | 22237685 | + |
| chr6H | 3 | 22238683 | 22238342 | + |
| chr6H | 4 | 22238974 | 22238862 | + |
| chr6H | 5 | 22239292 | 22239057 | + |
| chr6H | 6 | 22239749 | 22239402 | + |
| chr6H | 7 | 22240385 | 22239832 | + |
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 | 0.317101 |
| morex | ETI | 0 | 0 | 0.290993 |
| morex | LEA | 0.345261 | 0 | 0 |
| morex | EPI | 0 | 0.443286 | 0 |
| morex | ROO | 0 | 0 | 0.105292 |
| morex | ROO2 | 0 | 0 | 0.265444 |
| morex | NOD | 0 | 0 | 0 |
| morex | RAC | 0 | 0.193187 | 0 |
| morex | INF1 | 0.216438 | 0.359001 | 0.239108 |
| morex | INF2 | 0.632285 | 0.653145 | 0.954806 |
| morex | CAR5 | 2.32648 | 1.38505 | 2.28552 |
| morex | CAR15 | 0.571585 | 0.706082 | 0.440078 |
| morex | LEM | 0 | 0.161008 | 0.451433 |
| morex | LOD | 0 | 0 | 0 |
| morex | PAL | 0.23707 | 0.228678 | 0 |
| morex | SEN | 0.286387 | 0.478872 | 0 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03040.1 | +3 | 3e-98 | 305 | 190/231 (82%) | protein|RNA recognition motif containing protein, expressed |
| TAIR PP10 | AT5G52040 @ ARAPORT AT5G52040.4 @ TAIR |
+3 | 3e-65 | 219 | 144/255 (56%) | Symbols: RS41, At-RS41 | RNA-binding (RRM/RBD/RNP motifs) family protein | chr5:21131881-21133318 FORWARD LENGTH=324 |
| BRACH PP3 | Bradi3g02226.1.p | +3 | 3e-111 | 338 | 210/228 (92%) | pacid=32814082 transcript=Bradi3g02226.1 locus=Bradi3g02226 ID=Bradi3g02226.1.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 (2193 bp)
>BART1_0-u42531.004 2193 150831_barley_pseudomolecules ACCTGCCCCTGTCTGTCTCCGTCCTCCCCCCGCTCCACTCGCCGCCGGGTCCGAACCAGC CGCGCCCCCCGTCGAAAACCTAGGGTTCCGCCCTCCCCCGCCCCCTCCGAAGGTAACGCC GCGCACCCCCACCACGCCTCTCGCATGGCTGCCACGATCTCCTCCCCGCAGCACGGCGCC CGTCCTGCGCCCCGCCCCCTGGATCTGGCGCTCGCTCGGCCGCCTCGGCTGCAGGGAGCT CAGATCTGGCGATTTTTTCATATTTTTTTCTTCAATAGGACTCTAGCTCGCCTTTTGCTC TGCGTCGCTCCGTCTGAGCGGGCGCGCTGGCGGGTTCTGGGCATGCACGGGAGAGTTAGG TTCAGCTGCGCCGGACGTGGAAATCTGGCAACGGGGCCTGCCACCGAGAGAATCCGTGTG CTGTTTAAGCTGTGATGAAAATTCGCTCGTGGTTGTCAGGTTTGGGGAAGATCTGTTTAT ACAGCAACACCAACATGAGGCCAATTTTCTGCGGGAACCTTGACTATGATGCCCGCCAAT CTGAAGTCGAGCGTCTTTTTGGCAAATATGGAAGAGTGGAGCGAGTTGACATGAAGACAG GAATATCATGAAGCATCTGTGCTCTTCCTGGTTGATGGACTGGGCTCTACCTTTCCTGCC TGAGCCCCTGCCTCATGCCCTGTCCATTTCCAGGAGTTCACAGTCCACCATGACATCTGT CACTTGGAAACGACCACCTTGTGACTGATGTCTTACTTTTACATCAATGTTGCACCCTCC TCCCCCGCCCGGTTACACTCTCCCACGTCGACCAAACCATGCCAATCTCATGGCCGGCTG GAGAAGAGTAGAGGTTCCACCGGCAGCACCACCACCTCTTTTGGTGTACCACGAACGTTT GGATTATCGTACTCTGACATCATTTAGTGCAACATGCAAAAGGATTTGCGTTCGTCTACA TGGAAGATGAACGTGATGCTGAAGATGCTATCCGTAGACTTGATAGAACTGACTTTGGTA GAACAGGGAGGAGACTGAGAGTCGAATGGACAAAGGAGGATCGCAGTGGTGGTCGGAAAG GAAATGGAAAGAGATCTCCAAGCAGCGTGAAACCAACCAAAACCTTGTTTGTGATCAACT TTGATCCAATCAACACAAGGACAAGAGATCTGGAGAAGCACTTTGATCTGTATGGCAAGA TTGCAAATATCAGAATCAGAAGGAACTTTGCATTTGTCCAGTATGAAACACAGGAGGATG CTACTAAAGCTCTGGACGGTACTAATGGAAGCACTGTGATGGACAGGGTGATTTCTGTTG AGTATGCGCTTCGTGACGATGATGAAAAAAGGAACGGGTACAGTCCAGACAGGAGAGGAG GCCGTGATAGGTCTCCTGACAGAAGGGACAATCGTGGTAGGTCGGCAAGTCCTTATGGCA GAGGGCGGGAAAGGGGCAGCCCAGACTATGGCAGGGGCAGGGAGAGGGGCAGCCCGGACT ATGGCAAGGGCGGTGCCAGAGATAGTCCTGACTATGTCCGTGGTGGAAGCCCGTACGGCG GCAAAGGGGATGACAGGGCTAGCCCCAAGTATGACCGTGAACGCCGTGAAGCCAGTCCTG CCTATGACAGGCGCCGCAGCCGCTCGCCTGCAAGGGAAGATAGGGACTGAAGCTGTACCA TGGATGGCTGCGCTCAATCCTGGGTGCTTCGGACCAAATGGATGCACCGTCCTAGTGCGA TGTTCGCTCAAGTTGGTTATGTTAGGCAGCCAGGAACTTCTGTAATATCTCTCTATTAGC TAGCTCTAGCTGAATGCTTTGTCGATTTAGTTTGAACTGTGATTGTTAGCTTGAACTTTG TGCAAAGGGATTCTTCCGGTGAGACCATTTGCGGAGCGATGAGATGTACCGTGTATCGAC CGACAGCAGTATTCTAGCTTTGCACTTTGGTTATTCTTCCATATGTTCCTATTCTTCACT ATTGTTTCTGCTTGTGTGCTGGTCGACATGGTTGAGGATGGTGACCTTTGAGGAAGATAG AGGCTAATGTTGTGGTGGTGACGTCCATGGCTTCGGCAACATACTTCTTCTGTACCTAAA TAACTATAGTTCTTTTGTACCTAAATAGTTATAGTTGGGGAGAACTAGGTACTTCTGAAG TAGGAGAGAGGAGGGGTGGATGATGTGGTGGGA
Protein Sequence (236 aa)
>BART1_0-u42531.004 236 150831_barley_pseudomolecules MEDERDAEDAIRRLDRTDFGRTGRRLRVEWTKEDRSGGRKGNGKRSPSSVKPTKTLFVIN FDPINTRTRDLEKHFDLYGKIANIRIRRNFAFVQYETQEDATKALDGTNGSTVMDRVISV EYALRDDDEKRNGYSPDRRGGRDRSPDRRDNRGRSASPYGRGRERGSPDYGRGRERGSPD YGKGGARDSPDYVRGGSPYGGKGDDRASPKYDRERREASPAYDRRRSRSPAREDRD