- Transcript BART1_0-u24401.001
- Transcript IDBART1_0-u24401.001
- Gene IDBART1_0-u24401
Barley RTD
Exon Structure of BART1_0-u24401.001
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 659169943 | 659169703 | + |
| chr3H | 2 | 659171437 | 659171284 | + |
| chr3H | 3 | 659171629 | 659171536 | + |
| chr3H | 4 | 659172666 | 659172481 | + |
| chr3H | 5 | 659172823 | 659172776 | + |
| chr3H | 6 | 659173083 | 659172898 | + |
| chr3H | 7 | 659173257 | 659173171 | + |
| chr3H | 8 | 659173653 | 659173567 | + |
| chr3H | 9 | 659174781 | 659173736 | + |
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 | 0.447024 | 0.312762 |
| morex | ETI | 0.438726 | 0.185483 | 0.493551 |
| morex | LEA | 0.569799 | 0 | 0 |
| morex | EPI | 0.209749 | 0 | 0.146925 |
| morex | ROO | 0 | 0.288371 | 0.389981 |
| morex | ROO2 | 0.251555 | 0.15191 | 0.194953 |
| morex | NOD | 0.281798 | 0.523375 | 0.262868 |
| morex | RAC | 1.35938 | 0.175988 | 0.591198 |
| morex | INF1 | 2.20879 | 1.68619 | 0.947565 |
| morex | INF2 | 2.02224 | 2.7552 | 3.0223 |
| morex | CAR5 | 1.7099 | 1.27079 | 1.22633 |
| morex | CAR15 | 0 | 0.816748 | 1.27619 |
| morex | LEM | 0.240639 | 0.176021 | 0.310116 |
| morex | LOD | 0.269584 | 0.683829 | 0.734661 |
| morex | PAL | 0.569521 | 0.228328 | 0.316083 |
| morex | SEN | 0.314457 | 0 | 0 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os01g70920.2 | +1 | 3e-135 | 401 | 207/301 (69%) | protein|cullin-1, putative, expressed |
| TAIR PP10 | AT4G02570 @ ARAPORT AT4G02570.4 @ TAIR |
+1 | 3e-35 | 142 | 105/319 (33%) | Symbols: CUL1 | cullin 1 | chr4:1129315-1133435 FORWARD LENGTH=738 |
| BRACH PP3 | Bradi2g60057.3.p | +1 | 5e-159 | 461 | 236/304 (78%) | pacid=32775524 transcript=Bradi2g60057.3 locus=Bradi2g60057 ID=Bradi2g60057.3.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 (2129 bp)
>BART1_0-u24401.001 2129 150831_barley_pseudomolecules TTCGTGGAGACGTATGGAATTCTGTATTTTTGCCCATCAACAACTTAACTTTTCTTGATA AGAAAACAACTTAACTTTTCACAGATGTTATTAAGTGGGAGCGCACCAAAGAACCAAACC CCTCGAAAAAGCTGAAACCCGTCCCCCAATCCGCCGTCGGCTGCCCTCCTCACCCCTACC GCGAACGGCAGGCGAGACGGCGGCGGCGGCGAGCACCGCCCGATCCTCTCCCCCCTCGTC GTTCACTGTAGGAGCAAAGCAGTAAAAATGAATGCGCACCTCAGCTTTGAGGATGGCTGG AAGGTCCTGGAACAGGGCATTTTGACATGCTCAAAGATTTTGGAGGGTTCCACTGGTACA AGGCCTACTGTTGCTGAGTACATGAATTGCTATGACTGTGCTTATAGAATGGCTGTGCAG ACAACCAGCTATTGTGAAGAGATGTACAATGGTTACAGGACTACACTTGCAGAATCTGTT CGTGCACTGGTTTTACCCCATCTGATGCACAAGAGAGATGACTACCTTTTGAGACAGCTT GAGAAAATGTGGTCGAACTATTGTATCATGGTTAAATGTATATCTGGCTTCTTCAACTAT TTGGACCGTTGCTTTGTTGAGCAAAGAAAGCTACCTTGTCTTGAAGACACTGCTGCCACT TCTTTTTTCTCGACAGTCTTTTCGTTCTTTAGCCATGAAGTATCAGAGGCTCTACTGACT TTGATTCGCCAAGAGCGTGATGGAAGCAATGTTGATATGGACATCTTGATGGTCATTATG CGTGGCATATGTCGCTCTGAAGTCAAATCCTTCATGAGAAATGCTGTTGTCCAAGATACA TATGCTTACTACTCCAGGAAAAGTTCTGAATGGATAGTTCAGTACCCTCTACAAGATTAC CTTGCCATGGTCCAGGATTGTATGGAGAAGGAAACCATGAGATTGATGAGCTATCTGCAT ATTCCTGAGGGAGATAGCACAGAACTCTGTTTGAAGGTTGTTAGTGCTCCATTGATGCAA ATGTATGACAGCTATGCAAGAGAGAAACAGATTGGTGGCCAACTTTTGCTTCAAACATAC AAGACTGTGGAGGATGATCTGCTGGCCAGATGCAATCGCTTGACAATTGACAGCGGCGTG GACAACAGTTCTGGCAGTTACATGGAGTAGAAAGGAAATGCACTTCAGCTAACATTCATC TATAACCAAGATTACATACAGGAAGGGGTTCTAGAACATGGCCTACATCTGGGGGAATTT TTTGTGCGGCTGCTCGGTTTTTGGTACCGTGGATTTTGTTGGCAAGGTTCGCCTAGATTA AACGCTGTACTGAATGCGAAGGGGATACCTCTTAAGTGCTGCCTCCTACCCCATTATGGT CAACAGCATCTGAAATGTACAGGATGGCTGGTCAATTTATGCCAATGGCAGTTTATTTTG ATCGTTGTCTAGCGAACATTAGGCCGGTCAGCACCTAGCACTCTTAGTGGCTGGACATGG AGTATGTGGTCATGACACCAGAATGATCGGTGCATTGCCTGTGTGCCTTTTGCTTGCGAG CTTCTGATGCTGTCTATGGTCTAAGCTTATCTATGACTTGATGTTACTTTCCTGTGTTTG TGTGCTTGCCTAAATTGCTAAACTGTAGGTTGGATGTGTTTTCGCTTATTTCATGTCAAG TTTGCTGTTATGGTTGCAGTTCTTTCCTTGGTGGGCCATAATTGTTTGCAATTTTAGATT AGATTATAAACCCTGGTTCCATTATTAATGGGGCATGGATCTTATACCTTGTTGGTCTGA CTTTAAGCTATTCTTGCGGCATATCCATTTTCTTGAATTAATAAAGTGCTCTTTGTTGGT CTTGCTTGCCGTTGCTCACAGCCTGGTGCTCGACCGTATTGTACCTGCCGTCCGTGAGCA CCTCAGTTGAGGAGGTAGGCGGCAAGGGCGTGCGGCACTGGGCACCACCCAAGCGCTGTC CTTGAGCACCTGCAGACCCGTGCGGCCACCCAGGCGCTGGAGCATGGTGATCACACTCCC GTTGGTGTGCACACTGAGCCCCAGCACCAGGTTCGTCCGTGGCCATGGCGCGTAGGCGTA GAAGTTCATCTGCACCACTTGTGCGTCCG
Protein Sequence (300 aa)
>BART1_0-u24401.001 300 150831_barley_pseudomolecules MNAHLSFEDGWKVLEQGILTCSKILEGSTGTRPTVAEYMNCYDCAYRMAVQTTSYCEEMY NGYRTTLAESVRALVLPHLMHKRDDYLLRQLEKMWSNYCIMVKCISGFFNYLDRCFVEQR KLPCLEDTAATSFFSTVFSFFSHEVSEALLTLIRQERDGSNVDMDILMVIMRGICRSEVK SFMRNAVVQDTYAYYSRKSSEWIVQYPLQDYLAMVQDCMEKETMRLMSYLHIPEGDSTEL CLKVVSAPLMQMYDSYAREKQIGGQLLLQTYKTVEDDLLARCNRLTIDSGVDNSSGSYME