- Transcript BART1_0-u35917.004
- Transcript IDBART1_0-u35917.004
- Gene IDBART1_0-u35917
Barley RTD
Exon Structure of BART1_0-u35917.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 428280957 | 428280725 | + |
| chr5H | 2 | 428281973 | 428281841 | + |
| chr5H | 3 | 428282415 | 428282078 | + |
| chr5H | 4 | 428282708 | 428282511 | + |
| chr5H | 5 | 428283382 | 428283299 | + |
| chr5H | 6 | 428283709 | 428283628 | + |
| chr5H | 7 | 428283911 | 428283785 | + |
| chr5H | 8 | 428284671 | 428284091 | + |
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 | 4.10398 | 2.3642 | 1.80751 |
| morex | ETI | 3.63438 | 2.07552 | 3.39087 |
| morex | LEA | 4.0226 | 4.3134 | 1.68555 |
| morex | EPI | 0.0108277 | 2.27014 | 1.43962 |
| morex | ROO | 1.60666 | 0 | 0 |
| morex | ROO2 | 1.82218 | 4.59228 | 4.36319 |
| morex | NOD | 0.845906 | 0.497778 | 0.0093321 |
| morex | RAC | 3.14694 | 2.68444 | 2.89169 |
| morex | INF1 | 2.68682 | 3.34069 | 5.51922 |
| morex | INF2 | 1.60204 | 0.921048 | 0.000000101872 |
| morex | CAR5 | 0 | 4.78245 | 0.160745 |
| morex | CAR15 | 0.706374 | 2.77082 | 0 |
| morex | LEM | 2.8461 | 2.63645 | 1.30366 |
| morex | LOD | 5.66872 | 3.38718 | 6.05246 |
| morex | PAL | 2.15714 | 2.21259 | 2.62688 |
| morex | SEN | 0.253185 | 2.87558 | 2.37508 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os09g12800.1 | +1 | 1e-105 | 321 | 232/280 (83%) | protein|zinc finger Ran-binding domain-containing protein 2, putative, expressed |
| TAIR PP10 | AT1G50300 @ ARAPORT AT1G50300.1 @ TAIR |
+1 | 7e-81 | 259 | 192/279 (69%) | Symbols: TAF15 | TBP-associated factor 15 | chr1:18628818-18631662 REVERSE LENGTH=372 |
| BRACH PP3 | Bradi1g19280.1.p | +1 | 2e-110 | 335 | 248/279 (89%) | pacid=32805605 transcript=Bradi1g19280.1 locus=Bradi1g19280 ID=Bradi1g19280.1.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 (1776 bp)
>BART1_0-u35917.004 1776 150831_barley_pseudomolecules CAGAAGCCCAGCATCTCAGCCTGCCCTGCCCTCGCCCTAATTGCGTGTGCCCATCGCCCA CGAAACGCCATCCCCAAGCACGCAGTGAGCGCTGAGATCCGCCCAAACCTAGCGCCGTCG CGGCTTCTCAACCACGCGGCCGCCGCCGCGTTCCCGTCGGCAGAGCACGAGGCGCGCGGT CCTCCGCGCACGCCTTCGATCCGCGCCGTCAACCTCGGCGCATCCCGGACTAGATGGCTG GATATATGTCTCGCGGACCCCCAAATGGCTCTATTTATGTATGCAATCTGCCTCCTGGAA CTGATGAGACCATGTTGGCTGAATATTTTGGCACCATAGGGTTGCTAAAGGTATGGGTCT TACCAGAAGGACAAAAGGACTGGCCACCCAAAGATTTGGATATACAGGGACAAAGTTACA AATGAACCAAAGGGTGATGCAACAGTCACCTATGAAGATCCCCATGCTGCTTCAGCTGCT GTGGAATGGTTCAACAATAAGGATTTCCATGGAAGCATCATCCAGGTTCACATAGCTGAG TCAAAAAACAAAGACACAGTTGATAACTTCACCAATGTGAGCGTCGATGCTGAGATTGTT GGACAAGATGAATTGGATAACGGGTCAGGCAGGGGTAGAGGACGTGGTGATGGTCCAGCA AAAGCTTGGCAGCAAGATGGAGATTGGATGTGTCCAAATACAAGCTGTGGCAATGTAAAT TTTGCCTTCCGTGGTGTGTGTAATCGTTGTGGAGCCTCTCGCCCTGCTGGTGTTAGTGGA TCAGGTGGTGGTGGTGGTAGGGGTAGAGGCCGTGGTAGTGATGATGCAAGAGGCAGTCGT GCTGCTGCTGCTGTTGGTGGTCCTCCTGGGCTGTTTGGTCCTAATGATTGGCCATGTACG ATGTGTGGCAATGTAAACTGGGCCAAGCGGACCAAATGTAATGTCTGTAACACCTCTAGG CCAGGTCACAATGAAGGTGGTGTGAGAGGTGGCCGGGGTGGCGGCTTTAAAGAACTTGAT GAAGAAGAACTAGAAGAAGTACGGAGGCGCCGGAAAGAAGCTGAGGAGGATGATGGAGAA ATGTATGATGAATTTGGTAACCTGAAAAAGAAGTTCCGTGCTAAGTCACATCAAACTGAG AGTACACCAACTCTTCCTGGGTCTGGACGTGCTGGATGGGAAGTTGAGCACCGTGGTTCC ACTGAGAGAGAAGGCCGAGAGAGGAGCAGAGATCGGGGCAGGGACGACTACGATGAAAGG GAAAGCAAGAACAGAGACAGAGGTTCTCATGGAAGAGAGCGGCGCCGTAGCCGAAGCAGG AGCAGAGACCGCGAGAAGGAGAGGGGGAGGGACAGGGGCAGAGATCGTGGCAACGAGAGA AGCTGGGAGCGCGGCACTGATCGTGAACGTGATCGCTACAGATGATATGTCAGGAGTTTT GTCATGTTTGCTTGCCACTTTTCGGTTTTCTGAACCTTTTGTTATGCTGTTGGAGAGCTG TGGTGTATCACACTGTTATCATTAACATGGGACAAGCTTATTATGTTTGGGTCTAAAGTT CTCAAAACAGACCGGATCGATGGGTCGTCAGATCATCTGGTACAACGGACCCATCAGATC ATCTGGTACATCAACGGAATTGCCGAGGAATGACCATCGAGACCTGAAAAAGTCTGGATC ATAGTATCCTTGCGGCATGAGCAGCATTTGTTCTGAAACAGAGCACCACCTCGAACTCGC TGAACAACCATGCACCGTAGATCCAGTGGTGCGGTG
Protein Sequence (245 aa)
>BART1_0-u35917.004 245 150831_barley_pseudomolecules MCPNTSCGNVNFAFRGVCNRCGASRPAGVSGSGGGGGRGRGRGSDDARGSRAAAAVGGPP GLFGPNDWPCTMCGNVNWAKRTKCNVCNTSRPGHNEGGVRGGRGGGFKELDEEELEEVRR RRKEAEEDDGEMYDEFGNLKKKFRAKSHQTESTPTLPGSGRAGWEVEHRGSTEREGRERS RDRGRDDYDERESKNRDRGSHGRERRRSRSRSRDREKERGRDRGRDRGNERSWERGTDRE RDRYR