- Transcript BART1_0-u24401.002
- Transcript IDBART1_0-u24401.002
- Gene IDBART1_0-u24401
Barley RTD
Exon Structure of BART1_0-u24401.002
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 659169943 | 659169703 | + |
| chr3H | 2 | 659171169 | 659171046 | + |
| chr3H | 3 | 659171437 | 659171284 | + |
| chr3H | 4 | 659171629 | 659171536 | + |
| chr3H | 5 | 659172666 | 659172481 | + |
| chr3H | 6 | 659172823 | 659172776 | + |
| chr3H | 7 | 659173083 | 659172898 | + |
| chr3H | 8 | 659173257 | 659173171 | + |
| chr3H | 9 | 659173653 | 659173567 | + |
| chr3H | 10 | 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 | 0.369094 | 0.59515 | 0 |
| morex | ETI | 0.25515 | 0.349247 | 0.230805 |
| morex | LEA | 0.329042 | 0.406956 | 0.340337 |
| morex | EPI | 0 | 0.168669 | 0.40684 |
| morex | ROO | 0 | 0.855725 | 0 |
| morex | ROO2 | 0.271064 | 0.369799 | 0.663189 |
| morex | NOD | 0.557255 | 1.07137 | 1.81427 |
| morex | RAC | 0 | 0.599626 | 0 |
| morex | INF1 | 1.84872 | 0.407547 | 1.54173 |
| morex | INF2 | 0.512391 | 3.83184 | 2.76535 |
| morex | CAR5 | 1.64885 | 0.391844 | 0.835333 |
| morex | CAR15 | 1.63341 | 2.48217 | 2.277 |
| morex | LEM | 1.22066 | 0.301793 | 0.508865 |
| morex | LOD | 0.240127 | 0.378885 | 0.306157 |
| morex | PAL | 0.288555 | 0.26138 | 0.209993 |
| morex | SEN | 0.513814 | 0.549495 | 0.210072 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os01g70920.2 | +2 | 1e-134 | 400 | 207/301 (69%) | protein|cullin-1, putative, expressed |
| TAIR PP10 | AT4G02570 @ ARAPORT AT4G02570.4 @ TAIR |
+2 | 6e-35 | 142 | 107/320 (33%) | Symbols: CUL1 | cullin 1 | chr4:1129315-1133435 FORWARD LENGTH=738 |
| BRACH PP3 | Bradi2g60057.3.p | +2 | 6e-159 | 463 | 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 (2253 bp)
>BART1_0-u24401.002 2253 150831_barley_pseudomolecules TTCGTGGAGACGTATGGAATTCTGTATTTTTGCCCATCAACAACTTAACTTTTCTTGATA AGAAAACAACTTAACTTTTCACAGATGTTATTAAGTGGGAGCGCACCAAAGAACCAAACC CCTCGAAAAAGCTGAAACCCGTCCCCCAATCCGCCGTCGGCTGCCCTCCTCACCCCTACC GCGAACGGCAGGCGAGACGGCGGCGGCGGCGAGCACCGCCCGATCCTCTCCCCCCTCGTC GAGGTTGCGGCCTGGTTTCCTAAATGGGTGCATGAAGGTTTCTGGAACATTTGTGTACTT GTGAAATTAGGGCTATCGTTTGTAGGGTATTGTGGGCCTTTGTTGAGTTTGTGTATCCAA CTAAGTTCACTGTAGGAGCAAAGCAGTAAAAATGAATGCGCACCTCAGCTTTGAGGATGG CTGGAAGGTCCTGGAACAGGGCATTTTGACATGCTCAAAGATTTTGGAGGGTTCCACTGG TACAAGGCCTACTGTTGCTGAGTACATGAATTGCTATGACTGTGCTTATAGAATGGCTGT GCAGACAACCAGCTATTGTGAAGAGATGTACAATGGTTACAGGACTACACTTGCAGAATC TGTTCGTGCACTGGTTTTACCCCATCTGATGCACAAGAGAGATGACTACCTTTTGAGACA GCTTGAGAAAATGTGGTCGAACTATTGTATCATGGTTAAATGTATATCTGGCTTCTTCAA CTATTTGGACCGTTGCTTTGTTGAGCAAAGAAAGCTACCTTGTCTTGAAGACACTGCTGC CACTTCTTTTTTCTCGACAGTCTTTTCGTTCTTTAGCCATGAAGTATCAGAGGCTCTACT GACTTTGATTCGCCAAGAGCGTGATGGAAGCAATGTTGATATGGACATCTTGATGGTCAT TATGCGTGGCATATGTCGCTCTGAAGTCAAATCCTTCATGAGAAATGCTGTTGTCCAAGA TACATATGCTTACTACTCCAGGAAAAGTTCTGAATGGATAGTTCAGTACCCTCTACAAGA TTACCTTGCCATGGTCCAGGATTGTATGGAGAAGGAAACCATGAGATTGATGAGCTATCT GCATATTCCTGAGGGAGATAGCACAGAACTCTGTTTGAAGGTTGTTAGTGCTCCATTGAT GCAAATGTATGACAGCTATGCAAGAGAGAAACAGATTGGTGGCCAACTTTTGCTTCAAAC ATACAAGACTGTGGAGGATGATCTGCTGGCCAGATGCAATCGCTTGACAATTGACAGCGG CGTGGACAACAGTTCTGGCAGTTACATGGAGTAGAAAGGAAATGCACTTCAGCTAACATT CATCTATAACCAAGATTACATACAGGAAGGGGTTCTAGAACATGGCCTACATCTGGGGGA ATTTTTTGTGCGGCTGCTCGGTTTTTGGTACCGTGGATTTTGTTGGCAAGGTTCGCCTAG ATTAAACGCTGTACTGAATGCGAAGGGGATACCTCTTAAGTGCTGCCTCCTACCCCATTA TGGTCAACAGCATCTGAAATGTACAGGATGGCTGGTCAATTTATGCCAATGGCAGTTTAT TTTGATCGTTGTCTAGCGAACATTAGGCCGGTCAGCACCTAGCACTCTTAGTGGCTGGAC ATGGAGTATGTGGTCATGACACCAGAATGATCGGTGCATTGCCTGTGTGCCTTTTGCTTG CGAGCTTCTGATGCTGTCTATGGTCTAAGCTTATCTATGACTTGATGTTACTTTCCTGTG TTTGTGTGCTTGCCTAAATTGCTAAACTGTAGGTTGGATGTGTTTTCGCTTATTTCATGT CAAGTTTGCTGTTATGGTTGCAGTTCTTTCCTTGGTGGGCCATAATTGTTTGCAATTTTA GATTAGATTATAAACCCTGGTTCCATTATTAATGGGGCATGGATCTTATACCTTGTTGGT CTGACTTTAAGCTATTCTTGCGGCATATCCATTTTCTTGAATTAATAAAGTGCTCTTTGT TGGTCTTGCTTGCCGTTGCTCACAGCCTGGTGCTCGACCGTATTGTACCTGCCGTCCGTG AGCACCTCAGTTGAGGAGGTAGGCGGCAAGGGCGTGCGGCACTGGGCACCACCCAAGCGC TGTCCTTGAGCACCTGCAGACCCGTGCGGCCACCCAGGCGCTGGAGCATGGTGATCACAC TCCCGTTGGTGTGCACACTGAGCCCCAGCACCAGGTTCGTCCGTGGCCATGGCGCGTAGG CGTAGAAGTTCATCTGCACCACTTGTGCGTCCG
Protein Sequence (300 aa)
>BART1_0-u24401.002 300 150831_barley_pseudomolecules MNAHLSFEDGWKVLEQGILTCSKILEGSTGTRPTVAEYMNCYDCAYRMAVQTTSYCEEMY NGYRTTLAESVRALVLPHLMHKRDDYLLRQLEKMWSNYCIMVKCISGFFNYLDRCFVEQR KLPCLEDTAATSFFSTVFSFFSHEVSEALLTLIRQERDGSNVDMDILMVIMRGICRSEVK SFMRNAVVQDTYAYYSRKSSEWIVQYPLQDYLAMVQDCMEKETMRLMSYLHIPEGDSTEL CLKVVSAPLMQMYDSYAREKQIGGQLLLQTYKTVEDDLLARCNRLTIDSGVDNSSGSYME