- Transcript BART1_0-u42531.002
- Transcript IDBART1_0-u42531.002
- Gene IDBART1_0-u42531
Barley RTD
Exon Structure of BART1_0-u42531.002
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22236688 | 22236557 | + |
| chr6H | 2 | 22237825 | 22237685 | + |
| chr6H | 3 | 22238683 | 22238342 | + |
| chr6H | 4 | 22238974 | 22238862 | + |
| chr6H | 5 | 22239292 | 22239057 | + |
| chr6H | 6 | 22239749 | 22239402 | + |
| chr6H | 7 | 22240662 | 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 | 7.11967 | 6.90119 | 8.89658 |
| morex | ETI | 1.65673 | 3.84965 | 1.10676 |
| morex | LEA | 5.19879 | 3.54839 | 4.34377 |
| morex | EPI | 2.80788 | 7.91457 | 3.16138 |
| morex | ROO | 6.36448 | 4.85997 | 3.17515 |
| morex | ROO2 | 3.10918 | 3.85531 | 4.45375 |
| morex | NOD | 8.55883 | 7.69536 | 14.4612 |
| morex | RAC | 10.3444 | 10.7981 | 13.7742 |
| morex | INF1 | 18.4596 | 16.8131 | 17.8764 |
| morex | INF2 | 14.2302 | 17.453 | 18.982 |
| morex | CAR5 | 11.6679 | 8.48961 | 11.6724 |
| morex | CAR15 | 4.90733 | 3.22007 | 2.76757 |
| morex | LEM | 8.87582 | 9.46737 | 6.84936 |
| morex | LOD | 11.9715 | 15.5297 | 11.625 |
| morex | PAL | 7.52101 | 8.9335 | 11.1246 |
| morex | SEN | 4.97136 | 5.99168 | 5.45556 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03040.1 | +3 | 2e-98 | 305 | 190/231 (82%) | protein|RNA recognition motif containing protein, expressed |
| TAIR PP10 | AT5G52040 @ ARAPORT AT5G52040.4 @ TAIR |
+3 | 2e-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 | 2e-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 (2143 bp)
>BART1_0-u42531.002 2143 150831_barley_pseudomolecules CCCCTGCTCACGGGCCACGGACCTGCCCCTGTCTGTCTCCGTCCTCCCCCCGCTCCACTC GCCGCCGGGTCCGAACCAGCCGCGCCCCCCGTCGAAAACCTAGGGTTCCGCCCTCCCCCG CCCCCTCCGAAGGTTTGGGGAAGATCTGTTTATACAGCAACACCAACATGAGGCCAATTT TCTGCGGGAACCTTGACTATGATGCCCGCCAATCTGAAGTCGAGCGTCTTTTTGGCAAAT ATGGAAGAGTGGAGCGAGTTGACATGAAGACAGGAATATCATGAAGCATCTGTGCTCTTC CTGGTTGATGGACTGGGCTCTACCTTTCCTGCCTGAGCCCCTGCCTCATGCCCTGTCCAT TTCCAGGAGTTCACAGTCCACCATGACATCTGTCACTTGGAAACGACCACCTTGTGACTG ATGTCTTACTTTTACATCAATGTTGCACCCTCCTCCCCCGCCCGGTTACACTCTCCCACG TCGACCAAACCATGCCAATCTCATGGCCGGCTGGAGAAGAGTAGAGGTTCCACCGGCAGC ACCACCACCTCTTTTGGTGTACCACGAACGTTTGGATTATCGTACTCTGACATCATTTAG TGCAACATGCAAAAGGATTTGCGTTCGTCTACATGGAAGATGAACGTGATGCTGAAGATG CTATCCGTAGACTTGATAGAACTGACTTTGGTAGAACAGGGAGGAGACTGAGAGTCGAAT GGACAAAGGAGGATCGCAGTGGTGGTCGGAAAGGAAATGGAAAGAGATCTCCAAGCAGCG TGAAACCAACCAAAACCTTGTTTGTGATCAACTTTGATCCAATCAACACAAGGACAAGAG ATCTGGAGAAGCACTTTGATCTGTATGGCAAGATTGCAAATATCAGAATCAGAAGGAACT TTGCATTTGTCCAGTATGAAACACAGGAGGATGCTACTAAAGCTCTGGACGGTACTAATG GAAGCACTGTGATGGACAGGGTGATTTCTGTTGAGTATGCGCTTCGTGACGATGATGAAA AAAGGAACGGGTACAGTCCAGACAGGAGAGGAGGCCGTGATAGGTCTCCTGACAGAAGGG ACAATCGTGGTAGGTCGGCAAGTCCTTATGGCAGAGGGCGGGAAAGGGGCAGCCCAGACT ATGGCAGGGGCAGGGAGAGGGGCAGCCCGGACTATGGCAAGGGCGGTGCCAGAGATAGTC CTGACTATGTCCGTGGTGGAAGCCCGTACGGCGGCAAAGGGGATGACAGGGCTAGCCCCA AGTATGACCGTGAACGCCGTGAAGCCAGTCCTGCCTATGACAGGCGCCGCAGCCGCTCGC CTGCAAGGGAAGATAGGGACTGAAGCTGTACCATGGATGGCTGCGCTCAATCCTGGGTGC TTCGGACCAAATGGATGCACCGTCCTAGTGCGATGTTCGCTCAAGTTGGTTATGTTAGGC AGCCAGGAACTTCTGTAATATCTCTCTATTAGCTAGCTCTAGCTGAATGCTTTGTCGATT TAGTTTGAACTGTGATTGTTAGCTTGAACTTTGTGCAAAGGGATTCTTCCGGTGAGACCA TTTGCGGAGCGATGAGATGTACCGTGTATCGACCGACAGCAGTATTCTAGCTTTGCACTT TGGTTATTCTTCCATATGTTCCTATTCTTCACTATTGTTTCTGCTTGTGTGCTGGTCGAC ATGGTTGAGGATGGTGACCTTTGAGGAAGATAGAGGCTAATGTTGTGGTGGTGACGTCCA TGGCTTCGGCAACATACTTCTTCTGTACCTAAATAACTATAGTTCTTTTGTACCTAAATA GTTATAGTTGGGGAGAACTAGGTACTTCTGAAGTAGGAGAGAGGAGGGGTGGATGATGTG GTGGGAGCTTGGTTTTTATTTATTTATTTTTTGTCAAAGAAATGATAGAAAAAATATATT TGATTTAGTTATGTTGATTGATTTTGGTAAATGACAAGTTATGATTTGATATTTTTGGCC CTATGATTTGATTCCTTTAGGCGGGTTTTCAGAGTATTAACCCTGCGCGGCCCAGAAACC TCCCTAAGCCTCGACGACCCATTTGTTTCGTGTGTTTTGCACAGTCCAATCCATTTCATC CCCCTTGGATCCCCTCCTATCCACACGTCTTTCAAGCCTCGAG
Protein Sequence (236 aa)
>BART1_0-u42531.002 236 150831_barley_pseudomolecules MEDERDAEDAIRRLDRTDFGRTGRRLRVEWTKEDRSGGRKGNGKRSPSSVKPTKTLFVIN FDPINTRTRDLEKHFDLYGKIANIRIRRNFAFVQYETQEDATKALDGTNGSTVMDRVISV EYALRDDDEKRNGYSPDRRGGRDRSPDRRDNRGRSASPYGRGRERGSPDYGRGRERGSPD YGKGGARDSPDYVRGGSPYGGKGDDRASPKYDRERREASPAYDRRRSRSPAREDRD