- Transcript BART1_0-u25435.012
- Transcript IDBART1_0-u25435.012
- Gene IDBART1_0-u25435
Barley RTD
Exon Structure of BART1_0-u25435.012
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 681728097 | 681727663 | - |
| chr3H | 2 | 681728628 | 681728591 | - |
| chr3H | 3 | 681728830 | 681728758 | - |
| chr3H | 4 | 681729057 | 681728926 | - |
| chr3H | 5 | 681729385 | 681729308 | - |
| chr3H | 6 | 681729694 | 681729472 | - |
| chr3H | 7 | 681730030 | 681729865 | - |
| chr3H | 8 | 681730185 | 681730105 | - |
| chr3H | 9 | 681730317 | 681730271 | - |
| chr3H | 10 | 681730787 | 681730695 | - |
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 | 5.29306 | 3.60674 | 1.49325 |
| morex | ETI | 15.9201 | 8.01357 | 14.1203 |
| morex | LEA | 2.88983 | 0 | 3.60246 |
| morex | EPI | 5.36983 | 10.1607 | 5.14634 |
| morex | ROO | 0.000132508 | 1.87794 | 0.33818 |
| morex | ROO2 | 13.599 | 14.7931 | 13.73 |
| morex | NOD | 1.87047 | 9.41246 | 16.0442 |
| morex | RAC | 28.6777 | 28.5695 | 27.3048 |
| morex | INF1 | 5.28154 | 13.7548 | 10.5523 |
| morex | INF2 | 26.8182 | 19.7893 | 15.6353 |
| morex | CAR5 | 5.56948 | 9.09475 | 1.18444 |
| morex | CAR15 | 0.00000107132 | 0.0696599 | 0 |
| morex | LEM | 22.652 | 19.7618 | 14.603 |
| morex | LOD | 23.0461 | 32.7105 | 19.4178 |
| morex | PAL | 16.7668 | 14.0165 | 16.5999 |
| morex | SEN | 13.25 | 11.8435 | 12.0374 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os01g72890.2 | +3 | 1e-53 | 186 | 102/122 (84%) | protein|transposon protein, putative, CACTA, En/Spm sub-class, expressed |
| TAIR PP10 | AT1G16610 @ ARAPORT AT1G16610.1 @ TAIR |
+3 | 1e-40 | 150 | 81/115 (70%) | Symbols: SR45, RNPS1 | arginine/serine-rich 45 | chr1:5675925-5678686 REVERSE LENGTH=414 |
| BRACH PP3 | Bradi2g61380.4.p | +3 | 2e-55 | 191 | 109/123 (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 (1366 bp)
>BART1_0-u25435.012 1366 150831_barley_pseudomolecules TCAGGAAAGCATCTCCCCCTCCTCAGTCGGTTGTTCTACACGTTGATCATCTATCCAGAA ATGTGAATGAGGCTCATTTGAAGGAGATATTTGGAAGTTATGGCGAAGTGGTGAATGTGG AGCTATCAATGGACAAATTTGTTAATCTCCCTCGTGGGTATGGATACATCGAGTTCAAGA AGAGGACTGATGCTGAGAAGGCTCTTCTTTACATGGATGGTGGGCAAATTGATGGAAATG TTGTCAAGCTGAAGTTCACACTGCCACCACGCCAAAAGGCTTCTTCACCTTTAAAGCCAC CTCCTCCTCCCCCCAGAAGAGATGCTCCTCAGAATGATAAAGTTGCTATTGGTGCTGAAA AGGATGCGCAGCAGCGCCCTGGGGGATCATCTCCACGAAAGAAGCCACCTTCTCCTCCGC GAAAGAGGTCTCCTCCAAATAGAAGGGCTGAGTCACCCCGGCGTCCACCCAATCCATCTC CAAGGCGTCGTGCTGATTCTCCTATTCGTCGTCGACCAGATCTTTCCCCTGTTAGGCGTG GTGACAGAAGACCAGGATCTCCAATTAGAAGACGTTCCCCTTCACCTAGAAGGCATAGGT CACCAATGCGGAGGGGTCGTGGCAGCTTATCACCTCGCAGACGCTCCCCGGGGCCTCCTA GGCGCTCACCTGGGCCTCCCAGACGGCGCAGGTCACCACCACCAAGGAGATTGAGGAGTC CTCCAAGAAGGCCACCACCACCACCTCCCCGTCGTCACAGTCGCTCCCCTCCTCCTCGCC GCCCTCTTCACTCCCGCTCTAGATCGATTTCTCCTCGCAGGGGGCGAGGACCACCATTGA GGCGTGGAAGGTCGGATTCATCATATTCTGCATCACCCAGTCCTCCAAGAAAGGGACCAA GAAGGGTGTCAAGGAGCCGCAGCCCTAGAAGGCCTCCCAGAGGAAGGAGCGGATCTAGCG ACAGCGGGAGCAGCAGCTCTTCCCCAACCCCAAGGCGCAGGTAGAAAGAAAGAAACTCGT AACGTGTGTTGTTCCTGGCAGGTAAAAAAACTTTCTCTTCTCTCTCGACTGTCACCATGG ATTGCGTCTGCATGCATGTATCTTGCTGTGAGCTCAAGTCAAGAGGCGATCGATGTGAGG GGCGGGACGATGCGATGAGGTGCTCGGCATGCCTCCCTGGCATTTGTACTCACAAGACAG ACTGTATGATGACGACTTGTGTTGATGATTTGCCTGTACTGGAACTATTTTTTTATAATT CTGCGGTTGTTTGTCAACTACAAATCTGGCTAGTATTATTATCCTGTTGCCACTCTTGAG AATTAATGAGTTGTTTACTAGTTGATTGATGGATTGGCTCGTGGAG
Protein Sequence (333 aa)
>BART1_0-u25435.012 333 150831_barley_pseudomolecules RKASPPPQSVVLHVDHLSRNVNEAHLKEIFGSYGEVVNVELSMDKFVNLPRGYGYIEFKK RTDAEKALLYMDGGQIDGNVVKLKFTLPPRQKASSPLKPPPPPPRRDAPQNDKVAIGAEK DAQQRPGGSSPRKKPPSPPRKRSPPNRRAESPRRPPNPSPRRRADSPIRRRPDLSPVRRG DRRPGSPIRRRSPSPRRHRSPMRRGRGSLSPRRRSPGPPRRSPGPPRRRRSPPPRRLRSP PRRPPPPPPRRHSRSPPPRRPLHSRSRSISPRRGRGPPLRRGRSDSSYSASPSPPRKGPR RVSRSRSPRRPPRGRSGSSDSGSSSSSPTPRRR