- Transcript BART1_0-u12547.010
- Transcript IDBART1_0-u12547.010
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.010
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962607 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964276 | 554964158 | - |
| chr2H | 4 | 554964452 | 554964390 | - |
| chr2H | 5 | 554964980 | 554964530 | - |
| chr2H | 6 | 554965179 | 554965082 | - |
| chr2H | 7 | 554966070 | 554965968 | - |
| chr2H | 8 | 554967079 | 554966975 | - |
| chr2H | 9 | 554967248 | 554967169 | - |
| chr2H | 10 | 554967462 | 554967364 | - |
| chr2H | 11 | 554967652 | 554967557 | - |
| chr2H | 12 | 554968422 | 554968316 | - |
| chr2H | 13 | 554970201 | 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 | 6.0175 | 12.7078 | 14.9025 |
| morex | ETI | 7.49628 | 8.05374 | 8.66787 |
| morex | LEA | 7.86704 | 7.27448 | 7.37892 |
| morex | EPI | 2.76083 | 1.22721 | 4.00323 |
| morex | ROO | 5.31753 | 9.41062 | 4.151 |
| morex | ROO2 | 8.33261 | 9.71133 | 10.0099 |
| morex | NOD | 9.79642 | 8.94534 | 6.60536 |
| morex | RAC | 7.16319 | 8.45509 | 9.93256 |
| morex | INF1 | 16.9908 | 14.117 | 11.9103 |
| morex | INF2 | 21.8989 | 17.7987 | 14.4382 |
| morex | CAR5 | 20.1847 | 16.6249 | 19.4653 |
| morex | CAR15 | 6.83117 | 6.47513 | 7.76538 |
| morex | LEM | 12.0144 | 12.091 | 11.0347 |
| morex | LOD | 11.2484 | 13.4266 | 14.1909 |
| morex | PAL | 10.8329 | 7.12893 | 10.1177 |
| morex | SEN | 6.08986 | 8.02603 | 4.72509 |
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 | 676 | 407/514 (79%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+2 | 6e-84 | 279 | 204/524 (39%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +2 | 0.0 | 707 | 419/510 (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 (2850 bp)
>BART1_0-u12547.010 2850 150831_barley_pseudomolecules GATGGGTATTTTTCTCGTATCTTTGCTTGCGTTGCGCCTTCCCTTTTTTTTCCCCTTCCC GTGTCGCCTTTTCGTTTCGTCCTCGTCGTCGTCCTCCCTCTTCCACCCCCCTTCCCAATC TCCGACAGTTTCCAATTTCTCATCTCCCAACCCCAAACCCCAACCCCAACCAGAGACCGA AAAGAGTCGCACGCGACTTCGCGAGAGGGGGGAAGCAGCAGACGAGAGCGAGAGACCTCC TCCTTCCCCAACCCCGCCCCAAACCCTAACCCTTCATCAGATCTCGCGCCCGTCTGCCCT CCCGCCCCGTCCCGCCTCGATGTGACCCGGCCCCTAGGGTTTGTGCCGGCGCGGTGTGGT GGTGGGTCCCGGTTCGTGGGCGGATTTCGGACCCGAGGAGTTGGAGCTGGAGGCGCGCGC GCACATGAAGGACCCGGCGCACCGCACGAAGGTGGTGCTCAGGCGGCTGCCGCCGGCGAT TGCGCAGCAGGCCGTCGTGGACCAGGTTGACGCGCGCTTCGCTGGGCGCTATGACTGGGC CCGTTTCCGCCCCGGTAATGCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCTTAA CTTCAAGAGCCCAGAAGATGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATTTGT GAATGAAAAAGGTGCTCAATTTAAAGCTCTTGTGGAATATGCACCATCACAACAGGTTCC GAAGTCAAATATCAAGAAAGATGCTCGTCAAGGAACTATAACAAAAGATCCAGAATACTT GGAGTTTCTTGAGCTTATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAATTCAGCT TGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTACACCTCT TATGGTTTATGTTCGTCAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGTAAGTAG CAGACTAAGCAGAAAAGTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAAAAGGTC TTCTGAAAGGCGCAGGGCCTCCACTTCAACGCAGTATGTTGTGCGAGACAATGCTAAGGA AAAGCCGACTTACATCTTAGCACCAAAGAGAGATGATCATACACAGAGAGAGAAAATCAT TGCTGGAACTTCAGATGCTACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATCGACGG TAAAAGGGACAAAATTGTCCTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATTCTGTGCC CCCGTCGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAGTGG CAGAATTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCTCAACA TGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCCAAA CTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTATGATGA CAAGCATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACATGCCAG AAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGCATC AGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTATGGA CAATGTATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCCTGG TGGCCGCGGTGGCCTTGTGGAGAATGGAAACAGGCACCCCAACCGCCGTGGTCCGCCACG TGGGCCGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGGG CCCTGCTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGATC GTGAGTTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGTC TCTGGATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTGT GAAGTGCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTT GATTTGATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCACCAGTAGGTAGCTCT CCATCACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGAT GGAAATTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATTTCCAAGACCCCTGGA GGCTATACACAAACCCGACGATTCATCAGTGATGGATGTACATATCTCTAGAGAAAGAAG AGGTCTGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAAG AGTTACCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAGA ACCCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGCA AAGTGACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGTGAGGCTATTTTGCT TGCTGATGTTGTGTTTTCTACTGTGACGTCACTCACCATATAAGTTTTTTTGGGGTTACG TTAAGAATTATATGCATGGTTATGGTGTACGCCATCAAAGGTGGTTGCTGTTTTTATTAT CAGCAACAGGTATGTTTGACTTGCGCTGTTGATGTTCTGTCAGACAGGCAAGCTGTTGTT GTTAGTAATTCTTGTAAACACTTGCAGATCTGCCTATGGGTCGTGCGCGCACTGATCGGA GGAGGCAAAGTTCTCTTATTCTTGTAAGGG
Protein Sequence (499 aa)
>BART1_0-u12547.010 499 150831_barley_pseudomolecules MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR LSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVRDNAKEKPTYILAPKRDDHTQREKIIA GTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNSVPPSRNTPPSTSRQDQRNEASGR IIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVENAEKNHYDDK HNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFPLMQSHSMDN VSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRGPKEMEIPPIASDGKPSKRGP ASYVAHERQVWVQKSSSGS