- Transcript BART1_0-u12547.014
- Transcript IDBART1_0-u12547.014
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.014
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962800 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964452 | 554964158 | - |
| chr2H | 4 | 554964980 | 554964530 | - |
| chr2H | 5 | 554965179 | 554965082 | - |
| chr2H | 6 | 554966070 | 554965968 | - |
| chr2H | 7 | 554967079 | 554966975 | - |
| chr2H | 8 | 554967248 | 554967169 | - |
| chr2H | 9 | 554967462 | 554967364 | - |
| chr2H | 10 | 554967652 | 554967557 | - |
| chr2H | 11 | 554968422 | 554968182 | - |
| chr2H | 12 | 554970158 | 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 | 0.608933 | 1.16443 | 0.687193 |
| morex | ETI | 2.6125 | 2.70735 | 1.6314 |
| morex | LEA | 1.60579 | 2.5159 | 3.1775 |
| morex | EPI | 3.35096 | 5.76282 | 2.80113 |
| morex | ROO | 0.695783 | 0.886022 | 0.0249672 |
| morex | ROO2 | 0.700795 | 1.36336 | 1.043 |
| morex | NOD | 0.423928 | 2.1838 | 0.699395 |
| morex | RAC | 2.55556 | 2.69158 | 1.6969 |
| morex | INF1 | 2.12 | 3.54044 | 3.77183 |
| morex | INF2 | 4.97802 | 5.82551 | 7.13785 |
| morex | CAR5 | 3.60133 | 3.32196 | 5.64726 |
| morex | CAR15 | 0 | 1.12148 | 2.0477 |
| morex | LEM | 2.40568 | 1.22157 | 1.02986 |
| morex | LOD | 4.38973 | 3.20246 | 1.08734 |
| morex | PAL | 1.84324 | 2.57014 | 1.44397 |
| morex | SEN | 1.38771 | 1.4911 | 1.10538 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os04g35920.2 | +3 | 7e-177 | 466 | 289/376 (77%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+3 | 4e-67 | 154 | 127/330 (38%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +3 | 0.0 | 503 | 297/376 (79%) | 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 (2861 bp)
>BART1_0-u12547.014 2861 150831_barley_pseudomolecules TTTTTTTTCCCCTTCCCGTGTCGCCTTTTCGTTTCGTCCTCGTCGTCGTCCTCCCTCTTC CACCCCCCTTCCCAATCTCCGACAGTTTCCAATTTCTCATCTCCCAACCCCAAACCCCAA CCCCAACCAGAGACCGAAAAGAGTCGCACGCGACTTCGCGAGAGGGGGGAAGCAGCAGAC GAGAGCGAGAGACCTCCTCCTTCCCCAACCCCGCCCCAAACCCTAACCCTTCATCAGATC TCGCGCCCGTCTGCCCTCCCGCCCCGTCCCGCCTCGATGTGACCCGGCCCCTAGGGTTTG TGCCGGCGCGGTGTGGTGGTGGGTCCCGGTTCGTGGGCGGATTTCGGACCCGAGGAGTTG GAGCTGGAGGCGCGCGCGCACATGAAGGACCCGGCGCACCGCACGAAGGTGGTGCTCAGG CGGCTGCCGCCGGCGATTGCGCAGCAGGCCGTCGTGGACCAGGTTGACGCGCGCTTCGCT GGGCGCTATGACTGGGCCCGTTTCCGCCCCGGTAATGCCAGCCAAAAGAATCATAGATAT TCTCGTCTCTACCTTAACTTCAAGAGCCCAGAAGATGTTGTTGAGTTTGCTGAGTTCTTC AATGGGCATGTATTTGTGAATGAAAAAGGTATGTCCTTTATTTCTTAACCAATATGCTAT TTTTGTTTCATTTCTCATGTGCAATCAAGAGTATGCAGAACTCATATTCAGATTACGTCC ACTTATCGCTGTCCACGGTAGAGATATAAGTTCATTAGTGAGGTGCTCAATTTAAAGCTC TTGTGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAGAAAGATGCTCGTC AAGGAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTTATATCAAAGCCCA CTGAGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAGCTG CTGGAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGTCAGCAAAGGGCGG CTAAGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAAGTTGCAGGTGTGG TAACCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGGGCCTCCACTTCAA CGCAGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTAGCACCAAAGA GAGATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCTACAAGCGGAG GGCCATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTCCTCCTTAAAG GAAGAGCGAGGGTTGATTCCAATTCTGTGCCCCCGTCGAGAAATACACCTCCATCAACTT CTAGACAAGACCAGCGAAATGAGGCCAGTGGCAGAATTATCAAGACTATACTTTCAAACA AGGAAGGACGCCATGCAATAGCATCTCAACATGAGCAAGAAGGTCACATAATTAGTGCCG AGAAGGATAAGAGGCCACCACGGGCTCCAAACTCGCGTTCCACTGCAAAAGATCAGATTG TTGAAAATGCTGAGAAAAACCATTATGATGACAAGCATAATCATGTGCATGGTTCTGGAC CCATTGGTGAGAAGATTGAAAGACATGCCAGAAATAGAGATAGGCCTGACCGAGGTGTTT GGGCCCCTCGTCGCTATGACAAGTCTGCATCAGGAGGCGGTGCGCAAGCCTCATTGTCTG AGTTCCCGCTAATGCAGTCACACTCTATGGACAATGTATCTCAGCAAGTAGATGGCCATG GAGAGCGAAAAATAGACACAAGGGGTCCTGGTGGCCGCGGTGGCCTTGTGGAGAATGGTT TGTTTTTATCTGGTTATAAATAATAGTTAGCGATTAGGAAACAAGCAATCCAAAGTTTTT TCTATAGCAGTTTATGTACTATGCTTCATGGTGTAATATGCTATATTCAGGAAACAGGCA CCCCAACCGCCGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAATCCCTCCTATTGCATC TGATGGAAAGCCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCATGAGAGACAAGTATG GGTTCAGAAGTCAAGTTCAGGATCGTGAGTTTGTCCACCAATGATACTTTCATCAAAATA GATGTTGCAAGTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTCTGATTGTGAATGAAA TGACTGTTGGTGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGTCAACGGAAGTCTCAG CTATAGCTGAAAAAGCAGCTCTTTGATTTGATTCACAGAATCACAGCAATAGTGAAGTAA CATAACCCACCAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTTGATTTTGGACCCAAG GGTGCTATATCTGGAGGGACGGATGGAAATTAGGCTGGCATCAATACCTCGAGACAGTGG TCACATATTTCCAAGACCCCTGGAGGCTATACACAAACCCGACGATTCATCAGTGATGGA TGTACATATCTCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGTTTACAGGTTAGAGGT GCCATGTATCTACAAAGAGATAAGAGTTACCAGACTACCCAGTTTGCTAAATAAAGGTGA ATTTTTAGTTAGTTGATTATGAGAACCCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGTA AGACCGAAGTTACCGTGGAGTGCAAAGTGACAGCACTATCATGTTTTATGCTCCAGGTTG AATGGAATGTGAGGCTATTTTGCTTGCTGATGTTGTGTTTTCTACTGTGACGTCACTCAC CATATAAGTTTTTTTGGGGTTACGTTAAGAATTATATGCAT
Protein Sequence (296 aa)
>BART1_0-u12547.014 296 150831_barley_pseudomolecules MVYVRQQRAAKSMAQRSVSSRLSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVRDNAKE KPTYILAPKRDDHTQREKIIAGTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNSVP PSRNTPPSTSRQDQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPN SRSTAKDQIVENAEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSAS GGGAQASLSEFPLMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGLFLSGYK