- Transcript BART1_0-u25435.002
- Transcript IDBART1_0-u25435.002
- Gene IDBART1_0-u25435
Barley RTD
Exon Structure of BART1_0-u25435.002
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 681728628 | 681727258 | - |
| chr3H | 2 | 681728830 | 681728758 | - |
| chr3H | 3 | 681729057 | 681728926 | - |
| chr3H | 4 | 681729385 | 681729308 | - |
| chr3H | 5 | 681729694 | 681729472 | - |
| chr3H | 6 | 681730030 | 681729865 | - |
| chr3H | 7 | 681730185 | 681730105 | - |
| chr3H | 8 | 681730317 | 681730271 | - |
| chr3H | 9 | 681730783 | 681730695 | - |
| chr3H | 10 | 681731206 | 681731096 | - |
| chr3H | 11 | 681732647 | 681732395 | - |
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 | 0.446185 | 1.16047 | 0.731147 |
| morex | ETI | 0.154084 | 0.431695 | 0.207519 |
| morex | LEA | 0.179579 | 0.538624 | 0.411962 |
| morex | EPI | 0.375911 | 1.0786 | 0.23973 |
| morex | ROO | 0.436802 | 0.443034 | 0 |
| morex | ROO2 | 0.32703 | 0.264748 | 0.403621 |
| morex | NOD | 0.111651 | 0.258526 | 0 |
| morex | RAC | 0.803612 | 0.341745 | 0.308479 |
| morex | INF1 | 1.26147 | 0.802149 | 1.6509 |
| morex | INF2 | 1.4635 | 1.13879 | 2.23007 |
| morex | CAR5 | 1.69449 | 2.05165 | 2.19273 |
| morex | CAR15 | 0.7199 | 0.509946 | 0.661049 |
| morex | LEM | 0.0785862 | 0.171992 | 0.442178 |
| morex | LOD | 0.258336 | 0.245655 | 0.41294 |
| morex | PAL | 0.603678 | 0.15447 | 0.365822 |
| morex | SEN | 1.10324 | 0.621268 | 0.570524 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os01g72890.2 | +3 | 8e-49 | 180 | 98/117 (84%) | protein|transposon protein, putative, CACTA, En/Spm sub-class, expressed |
| TAIR PP10 | AT1G16610 @ ARAPORT AT1G16610.2 @ TAIR |
+3 | 5e-39 | 150 | 81/115 (70%) | Symbols: SR45, RNPS1 | arginine/serine-rich 45 | chr1:5675925-5678686 REVERSE LENGTH=407 |
| BRACH PP3 | Bradi2g61380.4.p | +3 | 2e-49 | 181 | 103/116 (89%) | pacid=32777636 transcript=Bradi2g61380.4 locus=Bradi2g61380 ID=Bradi2g61380.4.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 (2624 bp)
>BART1_0-u25435.002 2624 150831_barley_pseudomolecules ATATCCCCCCCGACCAAAACCCTAGCTCGCGCTCCAGACCCCGCACGCCCGCCGCCGCCG CGGGGAGACGGACGACGATGGCGAAGCCCCGCCGCGGCCGCTCAGGCTCGCGGTCCTCGT CGGGCTCCTCCTCCCGCTCCGCCTCCTCGGGCTCCTCCCGCTCGCGCTCGCGCTCCCGCT CCCGCTCCCTCTCCTCCTCCTCGTCCTCGCCCGCCCGCACCCGGGGCCGCTCCCCTCCCG CCGCCAAGCGCAGTTCACCTGGAGCAAAGAAAGGGCGATCACCTTCACCCCCTCTCAAAA AAGGGTCACCATCAAGGAAAGGCCGCTCAGCATCTCCCCCACCGAAGAAAGCTTCACCTC CTAGGAAAGCATCTCCCCCTCCTCAGTCGGTTGTTCTACACGTTGATCATCTATCCAGAA ATGTGAATGAGGCTCATTTGAAGGAGATATTTGGAAGTTATGGCGAAGTGGTGAATGTGG AGCTATCAATGGACAAATTTGTTAATCTCCCTCGTGGGTATGGATACATCGAGTTCAAGA AGAGGACTGATGCTGAGAAGGCTCTTCTTTACATGGATGGTGGGCAAATTGATGGAAATG TTGTCAAGCTGAAGTTCACACTGCCACCACGCCAAAAGGCTTCTTCACCTTTAAAGCCAC CTCCTCCTCCCCCCAGAAGAGATGCTCCTCAGAATGATAAAGTTGCTATTGGTGCTGAAA AGGATGCGCAGCAGCGCCCTGGGGGATCATCTCCACGAAAGAAGCCACCTTCTCCTCCGC GAAAGAGGTCTCCTCCAAATAGAAGGGCTGAGTCACCCCGGCGTCCACCCAATCCATCTC CAAGGCGTCGTGCTGATTCTCCTATTCGTCGTCGACCAGATCTTTCCCCTGTTAGGCGTG GTGACAGAAGACCAGGATCTCCAATTAGAAGACGTTCCCCTTCACCTAGAAGGCATAGGT CACCAATGCGGAGGGGTCGTGGCAGCTTATCACCTCGCAGACGCTCCCCGGGGCCTCCTA GGCGCTCACCTGGGCCTCCCAGACGGCGCAGGTCACCACCACCAAGGAGATTGAGGAGTC CTCCAAGAAGGCCACCACCACCACCTCCCCGTCGTCACAGTCGCTCCCCTCCTCCTCGCC GCCCTCTTCACTCCCGCTCTAGATCGATTTCTCCTCGCAGGGGGCGAGGACCACCATTGA GGCGTGGAAGGTCGGATTCATCATATTCTGCATCACCCAGTCCTCCAAGAAAGGGACCAA GAAGGGTGTCAAGGAGCCGCAGCCCTAGAAGGTATGTGACGGTTTTACATCCTTTGGCCT TTTGCATTTTTCCACATCTTGAAACGGAATTACTAGGTGTGGATTTTTGGAACCTGGGTG CACATGTACCCGATTTAGCAAATAAATAAATAAGTAACAGTCAAATATTTTGAAACATTT TTGCAATAAATGCTGTCTAGCGTATTACTCACGTGTAAAGTTCAGCGACAAACTGACTTC TGTGGTATTGTTGGCAAAAAAGACGAACTGTAGCTATAAAATATGTGAATAGTAAGGTTA ATATATTATTGATTTTGTTTTTGTTTGGGCAGAATACCCATGATATTCATTTTGTTGTGA AACTTTACAGTAGACAATCCTTGTTGCAAAACTAGTTTTAAAAATATTTGCCCCTTTTAC CTCTTTTTTTGCAATTCGGGTACATGTGCACCCATGTTGACTATGGTATTTTTATTACCA CAAGCTTATGTATGTAAAATTTAAAAAAATGGCATGTCTCTCAGGCCTCCCAGAGGAAGG AGCGGATCTAGCGACAGCGGGAGCAGCAGCTCTTCCCCAACCCCAAGGCGCAGGTAGAAA GAAAGAAACTCGTAACGTGTGTTGTTCCTGGCAGGTAAAAAAACTTTCTCTTCTCTCTCG ACTGTCACCATGGATTGCGTCTGCATGCATGTATCTTGCTGTGAGCTCAAGTCAAGAGGC GATCGATGTGAGGGGCGGGACGATGCGATGAGGTGCTCGGCATGCCTCCCTGGCATTTGT ACTCACAAGACAGACTGTATGATGACGACTTGTGTTGATGATTTGCCTGTACTGGAACTA TTTTTTTATAATTCTGCGGTTGTTTGTCAACTACAAATCTGGCTAGTATTATTATCCTGT TGCCACTCTTGAGAATTAATGAGTTGTTTACTAGTTGATTGATGGATTGGCTCGTGGAGT TGATTTTTCTTTAACTGTAGGTTTTGATTGTTTTGCATTTTGAACGTGCTTGGATGAATG TGCGTGAACCTGTTGCTCTGGCATGTCCGTCTCTATGAGCCCTGTTTGGTTTGGTGCTGG CGTATCTGTTTTGTTAGCGTCGAGGTTGAGCAACAGTCCTTGCCCCTGGCCATAGCAATC CCGGTGTGCTGGGATGCCACTGAAATGTTTAGGGATAGACAAAGCTGGTCATGCTGCTGA CATGTCTAAGCTGCGGATATGCTCTTAGAGCCTGTTCTGCAATCCACAAGAATGACACTT TGACGACAATGATAAGATGCGCTGCGGGGTGAGCAAAGCTGACTTTTCGGTGGTGCTCTG GCCGCTCCAGGAGAGGAGCGGAGCATAGAGCTGCCGAACAGGCT
Protein Sequence (443 aa)
>BART1_0-u25435.002 443 150831_barley_pseudomolecules MAKPRRGRSGSRSSSGSSSRSASSGSSRSRSRSRSRSLSSSSSSPARTRGRSPPAAKRSS PGAKKGRSPSPPLKKGSPSRKGRSASPPPKKASPPRKASPPPQSVVLHVDHLSRNVNEAH LKEIFGSYGEVVNVELSMDKFVNLPRGYGYIEFKKRTDAEKALLYMDGGQIDGNVVKLKF TLPPRQKASSPLKPPPPPPRRDAPQNDKVAIGAEKDAQQRPGGSSPRKKPPSPPRKRSPP NRRAESPRRPPNPSPRRRADSPIRRRPDLSPVRRGDRRPGSPIRRRSPSPRRHRSPMRRG RGSLSPRRRSPGPPRRSPGPPRRRRSPPPRRLRSPPRRPPPPPPRRHSRSPPPRRPLHSR SRSISPRRGRGPPLRRGRSDSSYSASPSPPRKGPRRVSRSRSPRRYVTVLHPLAFCIFPH LETELLGVDFWNLGAHVPDLANK