- Transcript BART1_0-u12547.016
- Transcript IDBART1_0-u12547.016
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.016
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962811 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964276 | 554964158 | - |
| chr2H | 4 | 554964452 | 554964390 | - |
| chr2H | 5 | 554965007 | 554964530 | - |
| chr2H | 6 | 554965179 | 554965082 | - |
| chr2H | 7 | 554966070 | 554965968 | - |
| chr2H | 8 | 554967079 | 554966975 | - |
| chr2H | 9 | 554967248 | 554967169 | - |
| chr2H | 10 | 554967462 | 554967364 | - |
| chr2H | 11 | 554967652 | 554967557 | - |
| chr2H | 12 | 554968528 | 554968316 | - |
| chr2H | 13 | 554970082 | 554969638 | - |
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 | 1.53674 | 0.574733 | 0 |
| morex | ETI | 4.83674 | 1.8016 | 3.88453 |
| morex | LEA | 1.68135 | 1.18659 | 0.00000396926 |
| morex | EPI | 1.11451 | 6.85101 | 2.52778 |
| morex | ROO | 1.58991 | 0.466147 | 0.0420232 |
| morex | ROO2 | 1.05809 | 1.50221 | 4.8524 |
| morex | NOD | 0 | 2.96526 | 0.00000137796 |
| morex | RAC | 9.29464 | 6.67342 | 7.3492 |
| morex | INF1 | 4.60245 | 5.7416 | 2.62427 |
| morex | INF2 | 2.30175 | 3.5859 | 4.9413 |
| morex | CAR5 | 1.58034 | 0 | 0 |
| morex | CAR15 | 1.32586 | 0.464513 | 0.0000000274685 |
| morex | LEM | 5.05838 | 6.88551 | 3.74062 |
| morex | LOD | 6.99905 | 7.88799 | 10.7347 |
| morex | PAL | 5.21406 | 6.88348 | 6.70622 |
| morex | SEN | 3.8466 | 5.87988 | 5.42786 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os04g35920.2 | +1 | 0.0 | 602 | 369/465 (79%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+1 | 5e-66 | 229 | 186/493 (38%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +1 | 0.0 | 642 | 383/465 (82%) | pacid=32810360 transcript=Bradi5g10820.2 locus=Bradi5g10820 ID=Bradi5g10820.2.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 (2660 bp)
>BART1_0-u12547.016 2660 150831_barley_pseudomolecules CTCCGACAGTTTCCAATTTCTCATCTCCCAACCCCAAACCCCAACCCCAACCAGAGACCG AAAAGAGTCGCACGCGACTTCGCGAGAGGGGGGAAGCAGCAGACGAGAGCGAGAGACCTC CTCCTTCCCCAACCCCGCCCCAAACCCTAACCCTTCATCAGATCTCGCGCCCGTCTGCCC TCCCGCCCCGTCCCGCCTCGATGTGACCCGGCCCCTAGGGTTTGTGCCGGCGCGGTGTGG TGGTGGGTCCCGGTTCGTGGGCGGATTTCGGACCCGAGGAGTTGGAGCTGGAGGCGCGCG CGCACATGAAGGACCCGGCGCACCGCACGAAGGTGGTGCTCAGGCGGCTGCCGCCGGCGA TTGCGCAGCAGGCCGTCGTGGACCAGGTTGACGCGCGCTTCGCTGGGCGCTATGACTGGG CCCGTTTCCGCCCCGGTAATGCCAGCCGATTTTACCTTAACTTCAAGAGCCCAGAAGATG TTGAGACAACAGTGACATAATTGTTTGCCACCATCTTTTTTCCAGTTGGTTAACTGATTT TTTATTTCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGCCCA GAAGATGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAAGGT GCTCAATTTAAAGCTCTTGTGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATC AAGAAAGATGCTCGTCAAGGAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAG CTTATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAA GCTGAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTT CGTCAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGA AAAGTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGC AGGGCCTCCACTTCAACGCAGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTAC ATCTTAGCACCAAAGAGAGATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCA GATGCTACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAA ATTGTCCTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATATATCTGATAGCTCAACCCCG CAGCAGTCTGTGCCCCCGTCGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCGA AATGAGGCCAGTGGCAGAATTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCA ATAGCATCTCAACATGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCA CCACGGGCTCCAAACTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAA AACCATTATGATGACAAGCATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATT GAAAGACATGCCAGAAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTAT GACAAGTCTGCATCAGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAG TCACACTCTATGGACAATGTATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGAC ACAAGGGGTCCTGGTGGCCGCGGTGGCCTTGTGGAGAATGGAAACAGGCACCCCAACCGC CGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAG CCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAG TCAAGTTCAGGATCGTGAGTTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCAA GTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGG TGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGA AAAAGCAGCTCTTTGATTTGATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCAC CAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATAT CTGGAGGGACGGATGGAAATTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATTT CCAAGACCCCTGGAGGCTATACACAAACCCGACGATTCATCAGTGATGGATGTACATATC TCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATC TACAAAGAGATAAGAGTTACCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTT AGTTGATTATGAGAACCCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGT TACCGTGGAGTGCAAAGTGACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGT GAGGCTATTTTGCTTGCTGATGTTGTGTTTTCTACTGTGACGTCACTCACCATATAAGTT TTTTTGGGGTTACGTTAAGA
Protein Sequence (349 aa)
>BART1_0-u12547.016 349 150831_barley_pseudomolecules MVYVRQQRAAKSMAQRSVSSRLSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVRDNAKE KPTYILAPKRDDHTQREKIIAGTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNISD SSTPQQSVPPSRNTPPSTSRQDQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEK DKRPPRAPNSRSTAKDQIVENAEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWA PRRYDKSASGGGAQASLSEFPLMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGNR HPNRRGPPRGPKEMEIPPIASDGKPSKRGPASYVAHERQVWVQKSSSGS