- Transcript BART1_0-u12547.022
- Transcript IDBART1_0-u12547.022
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.022
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962889 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964276 | 554964158 | - |
| chr2H | 4 | 554964452 | 554964390 | - |
| chr2H | 5 | 554965007 | 554964530 | - |
| chr2H | 6 | 554965179 | 554965082 | - |
| chr2H | 7 | 554966067 | 554965968 | - |
| chr2H | 8 | 554967079 | 554966975 | - |
| chr2H | 9 | 554967248 | 554967169 | - |
| chr2H | 10 | 554967462 | 554967364 | - |
| chr2H | 11 | 554967652 | 554967557 | - |
| chr2H | 12 | 554968243 | 554968182 | - |
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 | 12.4376 | 10.0839 | 11.2569 |
| morex | ETI | 9.70289 | 11.7543 | 13.2404 |
| morex | LEA | 9.97733 | 9.88405 | 11.5467 |
| morex | EPI | 10.7965 | 10.899 | 11.9557 |
| morex | ROO | 8.09993 | 7.2942 | 3.7528 |
| morex | ROO2 | 12.4313 | 11.6852 | 10.2555 |
| morex | NOD | 14.2556 | 14.4371 | 18.148 |
| morex | RAC | 17.2 | 15.9622 | 15.5666 |
| morex | INF1 | 18.3221 | 22.5572 | 23.5559 |
| morex | INF2 | 24.2692 | 26.5555 | 25.4555 |
| morex | CAR5 | 14.517 | 17.8314 | 15.8507 |
| morex | CAR15 | 0.0137139 | 1.02579 | 3.3335 |
| morex | LEM | 17.4116 | 16.8588 | 15.9335 |
| morex | LOD | 24.7878 | 19.3447 | 20.4172 |
| morex | PAL | 15.8406 | 16.2738 | 14.4428 |
| morex | SEN | 14.0155 | 15.1337 | 12.6861 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os04g35920.2 | +2 | 2e-179 | 520 | 326/428 (76%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.2 @ TAIR |
+2 | 3e-45 | 168 | 159/458 (35%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=484 |
| BRACH PP3 | Bradi5g10820.2.p | +2 | 0.0 | 571 | 349/427 (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 (1983 bp)
>BART1_0-u12547.022 1983 150831_barley_pseudomolecules CTCATATTCAGATTACGTCCACTTATCGCTGTCCACGGTAGAGATATAAGTTCATTAGTG AGGTGCTCAATTTAAAGCTCTTGTGGAATATGCACCATCACAACAGGTTCCGAAGTCAAA TATCAAGAAAGATGCTCGTCAAGGAACTATAACAAAAGATCCAGAATACTTGGAGTTTCT TGAGCTTATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAA AGAAGCTGAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTA TGTTCGTCAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAG CAGAAAAGTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAG GCGCAGGGCCTCCACTTCAACGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTA CATCTTAGCACCAAAGAGAGATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTC AGATGCTACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAA AATTGTCCTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATATATCTGATAGCTCAACCCC GCAGCAGTCTGTGCCCCCGTCGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCG AAATGAGGCCAGTGGCAGAATTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGC AATAGCATCTCAACATGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCC ACCACGGGCTCCAAACTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAA AAACCATTATGATGACAAGCATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGAT TGAAAGACATGCCAGAAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTA TGACAAGTCTGCATCAGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCA GTCACACTCTATGGACAATGTATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGA CACAAGGGGTCCTGGTGGCCGCGGTGGCCTTGTGGAGAATGGAAACAGGCACCCCAACCG CCGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAA GCCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAA GTCAAGTTCAGGATCGTGAGTTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCA AGTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTG GTGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTG AAAAAGCAGCTCTTTGATTTGATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCA CCAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATA TCTGGAGGGACGGATGGAAATTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATT TCCAAGACCCCTGGAGGCTATACACAAACCCGACGATTCATCAGTGATGGATGTACATAT CTCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTAT CTACAAAGAGATAAGAGTTACCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGT TAGTTGATTATGAGAACCCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAG TTACCGTGGAGTGCAAAGTGACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATG TGA
Protein Sequence (348 aa)
>BART1_0-u12547.022 348 150831_barley_pseudomolecules MVYVRQQRAAKSMAQRSVSSRLSRKVAGVVTSSSSPSKRSSERRRASTSTYVVRDNAKEK PTYILAPKRDDHTQREKIIAGTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNISDS STPQQSVPPSRNTPPSTSRQDQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKD KRPPRAPNSRSTAKDQIVENAEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAP RRYDKSASGGGAQASLSEFPLMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGNRH PNRRGPPRGPKEMEIPPIASDGKPSKRGPASYVAHERQVWVQKSSSGS