- Transcript BART1_0-u12547.013
- Transcript IDBART1_0-u12547.013
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.013
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962780 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964276 | 554964158 | - |
| chr2H | 4 | 554964452 | 554964390 | - |
| chr2H | 5 | 554964980 | 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 | 554968528 | 554968316 | - |
| chr2H | 13 | 554970137 | 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 | 0 | 0 |
| morex | ETI | 0 | 0 | 0 |
| morex | LEA | 0.000000079416 | 0 | 0 |
| morex | EPI | 0 | 0 | 0 |
| morex | ROO | 0.00000000369702 | 0 | 0 |
| morex | ROO2 | 0.0000549759 | 0 | 0 |
| morex | NOD | 0 | 0 | 0 |
| morex | RAC | 0 | 0 | 0 |
| morex | INF1 | 0 | 0 | 0 |
| morex | INF2 | 0 | 0 | 0 |
| morex | CAR5 | 0.00895094 | 0 | 0 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 0 | 0 | 0 |
| morex | LOD | 0 | 0 | 0 |
| morex | PAL | 0.0000000109727 | 0 | 0 |
| morex | SEN | 0 | 0 | 0 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os04g35920.2 | +2 | 0.0 | 576 | 353/465 (76%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+2 | 5e-65 | 226 | 183/481 (38%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +2 | 0.0 | 624 | 370/464 (80%) | 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 (2716 bp)
>BART1_0-u12547.013 2716 150831_barley_pseudomolecules CGCCTTTTCGTTTCGTCCTCGTCGTCGTCCTCCCTCTTCCACCCCCCTTCCCAATCTCCG ACAGTTTCCAATTTCTCATCTCCCAACCCCAAACCCCAACCCCAACCAGAGACCGAAAAG AGTCGCACGCGACTTCGCGAGAGGGGGGAAGCAGCAGACGAGAGCGAGAGACCTCCTCCT TCCCCAACCCCGCCCCAAACCCTAACCCTTCATCAGATCTCGCGCCCGTCTGCCCTCCCG CCCCGTCCCGCCTCGATGTGACCCGGCCCCTAGGGTTTGTGCCGGCGCGGTGTGGTGGTG GGTCCCGGTTCGTGGGCGGATTTCGGACCCGAGGAGTTGGAGCTGGAGGCGCGCGCGCAC ATGAAGGACCCGGCGCACCGCACGAAGGTGGTGCTCAGGCGGCTGCCGCCGGCGATTGCG CAGCAGGCCGTCGTGGACCAGGTTGACGCGCGCTTCGCTGGGCGCTATGACTGGGCCCGT TTCCGCCCCGGTAATGCCAGCCGATTTTACCTTAACTTCAAGAGCCCAGAAGATGTTGAG ACAACAGTGACATAATTGTTTGCCACCATCTTTTTTCCAGTTGGTTAACTGATTTTTTAT TTCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGCCCAGAAGA TGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAAGGTGCTCA ATTTAAAGCTCTTGTGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAGAA AGATGCTCGTCAAGGAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTTAT ATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCTGA AAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGTCA GCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAAGT TGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGGGC CTCCACTTCAACGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTAGC ACCAAAGAGAGATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCTAC AAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTCCT CCTTAAAGGAAGAGCGAGGGTTGATTCCAATTCTGTGCCCCCGTCGAGAAATACACCTCC ATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAGTGGCAGAATTATCAAGACTATACT TTCAAACAAGGAAGGACGCCATGCAATAGCATCTCAACATGAGCAAGAAGGTCACATAAT TAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCCAAACTCGCGTTCCACTGCAAAAGA TCAGATTGTTGAAAATGCTGAGAAAAACCATTATGATGACAAGCATAATCATGTGCATGG TTCTGGACCCATTGGTGAGAAGATTGAAAGACATGCCAGAAATAGAGATAGGCCTGACCG AGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGCATCAGGAGGCGGTGCGCAAGCCTC ATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTATGGACAATGTATCTCAGCAAGTAGA TGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCCTGGTGGCCGCGGTGGCCTTGTGGA GAATGGAAACAGGCACCCCAACCGCCGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAAT CCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCA TGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGTGAGTTTGTCCACCAATGAT ACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTC TGATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGT CAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGATTTGATTCACAGAATCACA GCAATAGTGAAGTAACATAACCCACCAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTT GATTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGATGGAAATTAGGCTGGCATCAAT ACCTCGAGACAGTGGTCACATATTTCCAAGACCCCTGGAGGCTATACACAAACCCGACGA TTCATCAGTGATGGATGTACATATCTCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGT TTACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAAGAGTTACCAGACTACCCAGTTT GCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAGAACCCCTGTATCCCGGCGGCTG CAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAAGTGACAGCACTATCATGTT TTATGCTCCAGGTTGAATGGAATGTGAGGCTATTTTGCTTGCTGATGTTGTGTTTTCTAC TGTGACGTCACTCACCATATAAGTTTTTTTGGGGTTACGTTAAGAATTATATGCATGGTT ATGGTGTACGCCATCA
Protein Sequence (339 aa)
>BART1_0-u12547.013 339 150831_barley_pseudomolecules MVYVRQQRAAKSMAQRSVSSRLSRKVAGVVTSSSSPSKRSSERRRASTSTYVVRDNAKEK PTYILAPKRDDHTQREKIIAGTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNSVPP SRNTPPSTSRQDQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNS RSTAKDQIVENAEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASG GGAQASLSEFPLMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRG PKEMEIPPIASDGKPSKRGPASYVAHERQVWVQKSSSGS