- Transcript BART1_0-u12547.009
- Transcript IDBART1_0-u12547.009
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.009
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554962669 | 554962575 | - |
| chr2H | 2 | 554963517 | 554962748 | - |
| chr2H | 3 | 554964049 | 554963996 | - |
| chr2H | 4 | 554964452 | 554964158 | - |
| chr2H | 5 | 554964983 | 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 | 554970170 | 554968316 | - |
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 | 0.138398 | 2.30598 | 0.788345 |
| morex | ETI | 1.94329 | 0.925212 | 0.810105 |
| morex | LEA | 0.748575 | 0.525181 | 1.59388 |
| morex | EPI | 1.19941 | 1.03197 | 1.11759 |
| morex | ROO | 0 | 1.07874 | 0.218892 |
| morex | ROO2 | 1.0034 | 0.935576 | 1.77606 |
| morex | NOD | 0.937656 | 1.13913 | 0.387385 |
| morex | RAC | 2.18225 | 2.22573 | 2.17801 |
| morex | INF1 | 4.04238 | 3.01974 | 3.09977 |
| morex | INF2 | 8.50275 | 5.8976 | 5.65731 |
| morex | CAR5 | 7.92473 | 6.54169 | 6.89879 |
| morex | CAR15 | 4.90461 | 4.35828 | 4.50415 |
| morex | LEM | 1.72541 | 1.17884 | 1.21382 |
| morex | LOD | 1.61794 | 1.01865 | 1.19627 |
| morex | PAL | 1.13313 | 0.725225 | 1.02829 |
| morex | SEN | 1.24601 | 1.43355 | 1.24297 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os04g35920.2 | +1 | 6e-179 | 541 | 318/413 (77%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+1 | 7e-62 | 220 | 156/372 (42%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +1 | 0.0 | 582 | 336/412 (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 (4101 bp)
>BART1_0-u12547.009 4101 150831_barley_pseudomolecules TTGCGCCTTCCCTTTTTTTTCCCCTTCCCGTGTCGCCTTTTCGTTTCGTCCTCGTCGTCG TCCTCCCTCTTCCACCCCCCTTCCCAATCTCCGACAGTTTCCAATTTCTCATCTCCCAAC CCCAAACCCCAACCCCAACCAGAGACCGAAAAGAGTCGCACGCGACTTCGCGAGAGGGGG GAAGCAGCAGACGAGAGCGAGAGACCTCCTCCTTCCCCAACCCCGCCCCAAACCCTAACC CTTCATCAGATCTCGCGCCCGTCTGCCCTCCCGCCCCGTCCCGCCTCGATGTGACCCGGC CCCTAGGGTTTGTGCCGGCGCGGTGTGGTGGTGGGTCCCGGTTCGTGGGCGGATTTCGGA CCCGAGGAGTTGGAGCTGGAGGCGCGCGCGCACATGAAGGACCCGGCGCACCGCACGAAG GTGGTGCTCAGGCGGCTGCCGCCGGCGATTGCGCAGCAGGCCGTCGTGGACCAGGTTGAC GCGCGCTTCGCTGGGCGCTATGACTGGGCCCGTTTCCGCCCCGGTAATGCCAGGTCAGCG TTTGCTCTCCCTCGCTCCCCGAGTCGTGCGAGTTGGAGCGTCTGCGAGGTTCGGTGCTCT TTAGGTCTGGATTGGGGTCGTGGCTGCTTAACATAGGAATTATGTGTAGGCGACTAGCAG TTTCCGTTTAGATTTCGTGTGCTGTTTAAGTGATGTAGTTTTTTTCGTTATTAGCATGCA TGTTCCATTTGTGTAATTGACATGTCTAGCTTCAAACTGTTGACACTATCTGGTGCAGCA TGTTATCCCTAGTTCTAGACTTGTAGTTGGTGTGTTTGTGAGGTTCGATGCTCTTTAGTT CTGGATTGGGGCCGTGGTTGTTGAACCTAGGAATTATGTGACTAGCAGTTTCTGGTTTCT CCCCTTAGATTTTGTGTGCTTGTATAAGTGTCAAGTGATGTAGTTTGTTTCGTTATTAGC AATCAGCATGTTCATTTGCCTAATTGAGATGTTAAGCTTAAAATTGTTGTTGCTATCTAG TGCAGAACGTTATTCCTAGTTGTGCACTTGTAGTTTACAGTGCAGTGCCACTTGCAGTTG CACTTCCTGCCTTCTTAGGTTCAACCAGAACGAACTGTCGGGTGTTAAATCGTAATTATG ATCTGTGCTTGTAATTTTGTTTTTTGAGTACAAATTTGTCGATGACTGTACCTTAAGTAT TAGTGAAGAATAGAGGTTGCCTTATTTGTTATGCAACTATCTACGCTTTCTACCTGTTAG TTCCATTTCTTCAGTTTGTTGCTGGCCTCACTGTTTTTTTATGGCAACTAAAAACGTAAA ATGTTCATTTTTTGCTTTCACTTATTTTGGATACAAGATCCATAATTCACTTATAGTGTG CTTTTTATGGAGCAATTCTTAAAAGAATCAGAAACACTTGAATTCAAAACTACCTTGTAG CATTCAGCCTTTTTACCTACCAGTCCTGTGCTATTGTCTGGTGATTTGTGCAGTAGTTTC TTCCTTAAATTTTGATGTCTTTGAGTTGCTTTTACTCAAAGTATAAGGCATCTTATTAGA ACCTAGCAGTGGGAAAACAATACTATATTTCTTGTTTGCCACCCTCTTTTGTCCAATTGG CTAACAAAATTTATCTATCCAGCCGATTTTACCTTAACTTCAAGAGCCCAGAAGATGTTG AGACAACAGTGACATAATTGTTTGCCACCATCTTTTTTCCAGTTGGTTAACTGATTTTTT ATTTCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGCCCAGAA GATGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAAGGTGCT CAATTTAAAGCTCTTGTGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAG AAAGATGCTCGTCAAGGAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTT ATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCT GAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGT CAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAA GTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGG GCCTCCACTTCAACGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTA GCACCAAAGAGAGATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCT ACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTC CTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATCAGTCTGTGCCCCCGTCGAGAAATACA CCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAGTGGCAGAATTATCAAGACT ATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCTCAACATGAGCAAGAAGGTCAC ATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCCAAACTCGCGTTCCACTGCA AAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTATGATGACAAGCATAATCATGTG CATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACATGCCAGAAATAGAGATAGGCCT GACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGCATCAGGAGGCGGTGCGCAA GCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTATGGACAATGTATCTCAGCAA GTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCCTGGTGGCCGCGGTGGCCTT GTGGAGAATGGTTTGTTTTTATCTGGTTATAAATAATAGTTAGCGATTAGGAAACAAGCA ATCCAAAGTTTTTTCTATAGCAGTTTATGTACTATGCTTCATGGTGTAATATGCTATATT CAGGAAACAGGCACCCCAACCGCCGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAATCC CTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCATG AGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGTGAGTTTGTCCACCAATGATAC TTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTCTG ATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGTCA ACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGATTTGATTCACAGAATCACAGC AATAGTGAAGTAACATAACCCACCAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTTGA TTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGATGGAAATTAGGCTGGCATCAATAC CTCGAGACAGTGGTCACATATTTCCAAGACCCCTGGAGGCTATACACAAACCCGACGATT CATCAGTGATGGATGTACATATCTCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGTTT ACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAAGAGTTACCAGACTACCCAGTTTGC TAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAGAACCCCTGTATCCCGGCGGCTGCA GTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAAGTGACAGCACTATCATGTTTT ATGCTCCAGGTTGAATGGAATGTGAGGCTATTTTGCTTGCTGATGTTGTGTTTTCTACTG TGACGTCACTCACCATATAAGTTTTTTTGGGGTTACGTTAAGAATTATATGCATGGTTAT GGTGTACGCCATCAAAGGTGGTTGCTGTTTTTATTATCAGCAACAGATCTGCCTATGGGT CGTGCGCGCACTGATCGGAGGAGGCAAAGTTCTCTTATTCTTGTAAGGGGAATTAGATCG TTCAATTAAACTACAAAGTCG
Protein Sequence (296 aa)
>BART1_0-u12547.009 296 150831_barley_pseudomolecules MVYVRQQRAAKSMAQRSVSSRLSRKVAGVVTSSSSPSKRSSERRRASTSTYVVRDNAKEK PTYILAPKRDDHTQREKIIAGTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNQSVP PSRNTPPSTSRQDQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPN SRSTAKDQIVENAEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSAS GGGAQASLSEFPLMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGLFLSGYK