- Transcript BART1_0-u12547.017
- Transcript IDBART1_0-u12547.017
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.017
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962812 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964452 | 554964158 | - |
| chr2H | 4 | 554964980 | 554964530 | - |
| chr2H | 5 | 554965179 | 554965082 | - |
| chr2H | 6 | 554966067 | 554965968 | - |
| chr2H | 7 | 554967079 | 554966975 | - |
| chr2H | 8 | 554967248 | 554967169 | - |
| chr2H | 9 | 554967462 | 554967364 | - |
| chr2H | 10 | 554967608 | 554967557 | - |
| chr2H | 11 | 554968858 | 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 | 2.048 | 1.3448 | 3.33384 |
| morex | ETI | 0.508186 | 0.517664 | 0.135012 |
| morex | LEA | 1.9698 | 0.616584 | 2.1943 |
| morex | EPI | 0.493586 | 0.000000328277 | 0.148862 |
| morex | ROO | 0.86508 | 1.34778 | 0.633055 |
| morex | ROO2 | 0.28485 | 0.745248 | 0.000445603 |
| morex | NOD | 1.66107 | 0 | 1.56953 |
| morex | RAC | 0.945851 | 0.00000000958941 | 1.12205 |
| morex | INF1 | 1.35181 | 2.9764 | 4.74553 |
| morex | INF2 | 0.547474 | 1.66372 | 0.755683 |
| morex | CAR5 | 0.000000000483989 | 0 | 0 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 0.489095 | 1.25927 | 0.321483 |
| morex | LOD | 0.216533 | 0.553761 | 1.45117 |
| morex | PAL | 0.316691 | 0 | 0.591255 |
| morex | SEN | 1.26811 | 0.770241 | 0.622952 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os04g35920.2 | +1 | 1e-141 | 430 | 265/363 (73%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+1 | 4e-43 | 129 | 114/316 (36%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +1 | 4e-159 | 474 | 281/362 (78%) | 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 (2583 bp)
>BART1_0-u12547.017 2583 150831_barley_pseudomolecules AACGTAAAATGTTCATTTTTTGCTTTCACTTATTTTGGATACAAGATCCATAATTCACTT ATAGTGTGCTTTTTATGGAGCAATTCTTAAAAGAATCAGAAACACTTGAATTCAAAACTA CCTTGTAGCATTCAGCCTTTTTACCTACCAGTCCTGTGCTATTGTCTGGTGATTTGTGCA GTAGTTTCTTCCTTAAATTTTGATGTCTTTGAGTTGCTTTTACTCAAAGTATAAGGCATC TTATTAGAACCTAGCAGTGGGAAAACAATACTATATTTCTTGTTTGCCACCCTCTTTTGT CCAATTGGCTAACAAAATTTATCTATCCAGCCGATTTTACCTTAACTTCAAGAGCCCAGA AGATGTTGAGACAACAGTGACATAATTGTTTGCCACCATCTTTTTTCCAGTTGGTTAACT GATTTTTTATTTCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCTTAACTTCAAGA GCCCAGAAGATGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAA AAGGTTCCGAAGTCAAATATCAAGAAAGATGCTCGTCAAGGAACTATAACAAAAGATCCA GAATACTTGGAGTTTCTTGAGCTTATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAA ATTCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATT ACACCTCTTATGGTTTATGTTCGTCAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCT GTAAGTAGCAGACTAAGCAGAAAAGTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCT AAAAGGTCTTCTGAAAGGCGCAGGGCCTCCACTTCAACGTATGTTGTGCGAGACAATGCT AAGGAAAAGCCGACTTACATCTTAGCACCAAAGAGAGATGATCATACACAGAGAGAGAAA ATCATTGCTGGAACTTCAGATGCTACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATC GACGGTAAAAGGGACAAAATTGTCCTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATTCT GTGCCCCCGTCGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCC AGTGGCAGAATTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCT CAACATGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCT CCAAACTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTAT GATGACAAGCATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACAT GCCAGAAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCT GCATCAGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCT ATGGACAATGTATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGT CCTGGTGGCCGCGGTGGCCTTGTGGAGAATGGTTTGTTTTTATCTGGTTATAAATAATAG TTAGCGATTAGGAAACAAGCAATCCAAAGTTTTTTCTATAGCAGTTTATGTACTATGCTT CATGGTGTAATATGCTATATTCAGGAAACAGGCACCCCAACCGCCGTGGTCCGCCACGTG GGCCGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCC CTGCTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGT GAGTTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTC TGGATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTGTGA AGTGCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGA TTTGATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCACCAGTAGGTAGCTCTCC ATCACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGATGG AAATTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATTTCCAAGACCCCTGGAGG CTATACACAAACCCGACGATTCATCAGTGATGGATGTACATATCTCTAGAGAAAGAAGAG GTCTGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAAGAG TTACCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAGAAC CCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAA GTGACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGTGAGGCTATTTTGCTTG CTGATGTTGTGTTTTCTACTGTGACGTCACTCACCATATAAGTTTTTTTGGGGTTACGTT AAG
Protein Sequence (360 aa)
>BART1_0-u12547.017 360 150831_barley_pseudomolecules MKKVPKSNIKKDARQGTITKDPEYLEFLELISKPTEHLPSAEIQLERKEAERAAAGKEPP VITPLMVYVRQQRAAKSMAQRSVSSRLSRKVAGVVTSSSSPSKRSSERRRASTSTYVVRD NAKEKPTYILAPKRDDHTQREKIIAGTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDS NSVPPSRNTPPSTSRQDQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPP RAPNSRSTAKDQIVENAEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYD KSASGGGAQASLSEFPLMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGLFLSGYK