- Transcript BART1_0-u12547.004
- Transcript IDBART1_0-u12547.004
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554962669 | 554962301 | - |
| chr2H | 2 | 554963517 | 554962748 | - |
| chr2H | 3 | 554964049 | 554963996 | - |
| chr2H | 4 | 554964276 | 554964158 | - |
| chr2H | 5 | 554964452 | 554964390 | - |
| chr2H | 6 | 554965007 | 554964530 | - |
| chr2H | 7 | 554965179 | 554965082 | - |
| chr2H | 8 | 554966067 | 554965968 | - |
| chr2H | 9 | 554967079 | 554966975 | - |
| chr2H | 10 | 554967248 | 554967169 | - |
| chr2H | 11 | 554967462 | 554967364 | - |
| chr2H | 12 | 554967652 | 554967557 | - |
| chr2H | 13 | 554968422 | 554968316 | - |
| chr2H | 14 | 554970169 | 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 | 0 | 0 |
| morex | EPI | 0 | 0 | 0 |
| morex | ROO | 0 | 0 | 0 |
| morex | ROO2 | 0 | 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 | 0.0137965 | 0 |
| morex | CAR15 | 0.0000385459 | 0.000000343925 | 0.0197197 |
| morex | LEM | 0 | 0 | 0 |
| morex | LOD | 0 | 0 | 0 |
| morex | PAL | 0 | 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 | +3 | 0.0 | 690 | 405/514 (79%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+3 | 4e-86 | 286 | 205/537 (38%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +3 | 0.0 | 729 | 424/509 (83%) | 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 (3070 bp)
>BART1_0-u12547.004 3070 150831_barley_pseudomolecules TGCGCCTTCCCTTTTTTTTCCCCTTCCCGTGTCGCCTTTTCGTTTCGTCCTCGTCGTCGT CCTCCCTCTTCCACCCCCCTTCCCAATCTCCGACAGTTTCCAATTTCTCATCTCCCAACC CCAAACCCCAACCCCAACCAGAGACCGAAAAGAGTCGCACGCGACTTCGCGAGAGGGGGG AAGCAGCAGACGAGAGCGAGAGACCTCCTCCTTCCCCAACCCCGCCCCAAACCCTAACCC TTCATCAGATCTCGCGCCCGTCTGCCCTCCCGCCCCGTCCCGCCTCGATGTGACCCGGCC CCTAGGGTTTGTGCCGGCGCGGTGTGGTGGTGGGTCCCGGTTCGTGGGCGGATTTCGGAC CCGAGGAGTTGGAGCTGGAGGCGCGCGCGCACATGAAGGACCCGGCGCACCGCACGAAGG TGGTGCTCAGGCGGCTGCCGCCGGCGATTGCGCAGCAGGCCGTCGTGGACCAGGTTGACG CGCGCTTCGCTGGGCGCTATGACTGGGCCCGTTTCCGCCCCGGTAATGCCAGCCAAAAGA ATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGCCCAGAAGATGTTGTTGAGTTTG CTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAAGGTGCTCAATTTAAAGCTCTTG TGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAGAAAGATGCTCGTCAAG GAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTTATATCAAAGCCCACTG AGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTG GAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGTCAGCAAAGGGCGGCTA AGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAAGTTGCAGGTGTGGTAA CCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGGGCCTCCACTTCAACGT ATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTAGCACCAAAGAGAGATG ATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCTACAAGCGGAGGGCCAT CTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTCCTCCTTAAAGGAAGAG CGAGGGTTGATTCCAATATATCTGATAGCTCAACCCCGCAGCAGTCTGTGCCCCCGTCGA GAAATACACCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAGTGGCAGAATTA TCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCTCAACATGAGCAAG AAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCCAAACTCGCGTT CCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTATGATGACAAGCATA ATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACATGCCAGAAATAGAG ATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGCATCAGGAGGCG GTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTATGGACAATGTAT CTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCCTGGTGGCCGCG GTGGCCTTGTGGAGAATGGAAACAGGCACCCCAACCGCCGTGGTCCGCCACGTGGGCCGA AGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCCCTGCTA GCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGTGAGTTT GTCCACCAATGATACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTCTGGATT TTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTGTGAAGTGCA ATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGATTTGAT TCACAGAATCACAGCAATAGTGAAGTAACATAACCCACCAGTAGGTAGCTCTCCATCACT TTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGATGGAAATTA GGCTGGCATCAATACCTCGAGACAGTGGTCACATATTTCCAAGACCCCTGGAGGCTATAC ACAAACCCGACGATTCATCAGTGATGGATGTACATATCTCTAGAGAAAGAAGAGGTCTGG CTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAAGAGTTACCA GACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAGAACCCCTGT ATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAAGTGACA GCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGTGAGGCTATTTTGCTTGCTGATG TTGTGTTTTCTACTGTGACGTCACTCACCATATAAGTTTTTTTGGGGTTACGTTAAGAAT TATATGCATGGTTATGGTGTACGCCATCAAAGGTGGTTGCTGTTTTTATTATCAGCAACA GATCTGCCTATGGGTCGTGCGCGCACTGATCGGAGGAGGCAAAGTTCTCTTATTCTTGTA AGGGGAATTAGATCGTTCAATTAAACTACAAAGTCGCTGGTTAACTACTTACAATGCAGC TGGGATCAATTTCTTCCCAAGAATAGTCATACTTAGCGAGTTTGTCAGCAACACCATAAC CATGCCTATTGAAAGGGAACGAAGAAGAAACAGGAAAAGGGAGTTCGGACTGTTACTTCG CCTAATATTGACCGTCCTGGTCCATCAAAAACCACTTTTCCCTTCCGCTCACCTGGTCGA GGATGGCCCTGTTGCATGTCTGGCTGAACACATTTCCTTGCCGCATTCAAATGTCTAACT TGCGTGGAAG
Protein Sequence (507 aa)
>BART1_0-u12547.004 507 150831_barley_pseudomolecules MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR LSRKVAGVVTSSSSPSKRSSERRRASTSTYVVRDNAKEKPTYILAPKRDDHTQREKIIAG TSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNISDSSTPQQSVPPSRNTPPSTSRQD QRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVENA EKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFPL MQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRGPKEMEIPPIASD GKPSKRGPASYVAHERQVWVQKSSSGS