- Transcript BART1_0-u12547.021
- Transcript IDBART1_0-u12547.021
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.021
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962885 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964269 | 554964158 | - |
| chr2H | 4 | 554964452 | 554964390 | - |
| 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 | 554968422 | 554968316 | - |
| chr2H | 13 | 554970024 | 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 | 2.96208 | 2.19211 |
| morex | ETI | 4.08806 | 2.00369 | 2.25457 |
| morex | LEA | 2.41726 | 3.19621 | 0.529634 |
| morex | EPI | 1.95411 | 3.40926 | 2.33404 |
| morex | ROO | 0 | 3.60818 | 0.969621 |
| morex | ROO2 | 3.79227 | 4.55774 | 4.77646 |
| morex | NOD | 1.69111 | 5.22533 | 2.7011 |
| morex | RAC | 10.4071 | 7.94047 | 6.93324 |
| morex | INF1 | 5.47001 | 2.87672 | 0.434646 |
| morex | INF2 | 0.939075 | 2.77977 | 4.24771 |
| morex | CAR5 | 2.51825 | 3.9102 | 2.47645 |
| morex | CAR15 | 2.40879 | 1.43114 | 0.00159164 |
| morex | LEM | 6.19139 | 7.65405 | 6.14145 |
| morex | LOD | 12.0944 | 6.60733 | 7.98165 |
| morex | PAL | 7.75581 | 7.80163 | 4.20769 |
| morex | SEN | 3.50774 | 4.04203 | 3.04729 |
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 | 637 | 367/474 (77%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+2 | 6e-84 | 276 | 178/417 (43%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +2 | 0.0 | 669 | 382/469 (81%) | 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 (2388 bp)
>BART1_0-u12547.021 2388 150831_barley_pseudomolecules CGAAAAGAGTCGCACGCGACTTCGCGAGAGGGGGGAAGCAGCAGACGAGAGCGAGAGACC TCCTCCTTCCCCAACCCCGCCCCAAACCCTAACCCTTCATCAGATCTCGCGCCCGTCTGC CCTCCCGCCCCGTCCCGCCTCGATGTGACCCGGCCCCTAGGGTTTGTGCCGGCGCGGTGT GGTGGTGGGTCCCGGTTCGTGGGCGGATTTCGGACCCGAGGAGTTGGAGCTGGAGGCGCG CGCGCACATGAAGGACCCGGCGCACCGCACGAAGGTGGTGCTCAGGCGGCTGCCGCCGGC GATTGCGCAGCAGGCCGTCGTGGACCAGGTTGACGCGCGCTTCGCTGGGCGCTATGACTG GGCCCGTTTCCGCCCCGGTAATGCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCT TAACTTCAAGAGCCCAGAAGATGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATT TGTGAATGAAAAAGGTGCTCAATTTAAAGCTCTTGTGGAATATGCACCATCACAACAGGT TCCGAAGTCAAATATCAAGAAAGATGCTCGTCAAGGAACTATAACAAAAGATCCAGAATA CTTGGAGTTTCTTGAGCTTATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAATTCA GCTTGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTACACC TCTTATGGTTTATGTTCGTCAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGTAAG TAGCAGACTAAGCAGAAAAGTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAAAAG GTCTTCTGAAAGGCGCAGGGCCTCCACTTCAACGTATGTTGTGCGAGACAATGCTAAGGA AAAGCCGACTTACATCTTAGCACCAAAGAGAGATGATCATACACAGAGAGAGAAAATCAT TGCTGGAACTTCAGATGCTACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATCGACGG TAAAAGGGACAAAATTGTCCTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATCAGTCTGT GCCCCCGTCGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAG TGGCAGAATTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCTCA ACATGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCC AAACTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTATGA TGACAAGCATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACATGC CAGAAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGC ATCAGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTAT GGACAATGTATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCC TGGTGGCCGCGGTGGCCTTGTGGAGAATGGCACCCCAACCGCCGTGGTCCGCCACGTGGG CCGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCCCT GCTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGTGA GTTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTCTG GATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTGTGAAG TGCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGATT TGATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCACCAGTAGGTAGCTCTCCAT CACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGATGGAA ATTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATTTCCAAGACCCCTGGAGGCT ATACACAAACCCGACGATTCATCAGTGATGGATGTACATATCTCTAGAGAAAGAAGAGGT CTGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAAGAGTT ACCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAGAACCC CTGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAAGT GACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGTGAGGCT
Protein Sequence (502 aa)
>BART1_0-u12547.021 502 150831_barley_pseudomolecules MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR LSRKVAGVVTSSSSPSKRSSERRRASTSTYVVRDNAKEKPTYILAPKRDDHTQREKIIAG TSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNQSVPPSRNTPPSTSRQDQRNEASGR IIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVENAEKNHYDDK HNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFPLMQSHSMDN VSQQVDGHGERKIDTRGPGGRGGLVENGTPTAVVRHVGRRRWKSLLLHLMESLRRGALLA MWLMRDKYGFRSQVQDREFVHQ