- Transcript BART1_0-u19873.005
- Transcript IDBART1_0-u19873.005
- Gene IDBART1_0-u19873
Barley RTD
Exon Structure of BART1_0-u19873.005
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 216303548 | 216303418 | + |
| chr3H | 2 | 216303945 | 216303843 | + |
| chr3H | 3 | 216304733 | 216304557 | + |
| chr3H | 4 | 216306264 | 216306038 | + |
| chr3H | 5 | 216306934 | 216306447 | + |
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 | 1.832 | 0.661766 | 1.85582 |
| morex | ETI | 8.65377 | 8.30564 | 5.47498 |
| morex | LEA | 3.1328 | 3.2125 | 4.65997 |
| morex | EPI | 8.86757 | 11.3166 | 10.2453 |
| morex | ROO | 1.14133 | 1.72905 | 0.839286 |
| morex | ROO2 | 2.83204 | 4.98053 | 3.79558 |
| morex | NOD | 2.88773 | 11.5423 | 11.5244 |
| morex | RAC | 9.45059 | 7.41838 | 6.33641 |
| morex | INF1 | 2.85456 | 3.50985 | 0.614333 |
| morex | INF2 | 3.50873 | 3.42284 | 1.44689 |
| morex | CAR5 | 2.02002 | 1.7827 | 3.21486 |
| morex | CAR15 | 1.26226 | 1.56814 | 1.63616 |
| morex | LEM | 6.20392 | 11.0318 | 6.84946 |
| morex | LOD | 12.4045 | 11.0434 | 11.8367 |
| morex | PAL | 6.64434 | 5.4508 | 7.90607 |
| morex | SEN | 7.9924 | 6.21212 | 4.48846 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os01g16210.1 | +3 | 1e-74 | 229 | 111/123 (90%) | protein|uncharacterized Cys-rich domain containing protein, putative, expressed |
| TAIR PP10 | AT2G40935 @ ARAPORT AT2G40935.1 @ TAIR |
+3 | 2e-70 | 219 | 102/166 (61%) | Symbols: | PLAC8 family protein | chr2:17083199-17084216 FORWARD LENGTH=190 |
| BRACH PP3 | Bradi2g09980.1.p | +3 | 1e-111 | 324 | 165/183 (90%) | pacid=32778952 transcript=Bradi2g09980.1 locus=Bradi2g09980 ID=Bradi2g09980.1.v3.1 annot-version=v3.1 |
Barley PseudoMolecules GBrowse
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grey: non-coding, green: Barley Morex IBSC 2017 Transcript CDS, red: Barley RTD exons
CDS Sequence (1126 bp)
>BART1_0-u19873.005 1126 150831_barley_pseudomolecules GTGGGCTGGGCCGTACTGTGCCAGCCCACTTGGCTAGGTTTGGCTGCATCGCCATGGTGG CTGAGGGAAAAACTTGGGCGAGCACCGACAGTTCCGCCGCGAATCTCAAAGCGCTGCGGC GGTTTCTCAAGCTCGGGCATTCGGCGGACAGAGCGTTCCGGAACTGGTGAGGCGAGGCCG CGGATAAGCACCAATTTGGTCGTCGGCGCTTCAGGGGTCTTTACCGATTTATTGAGATGG TTGGAAAAGGAAGCTATGTTCCGCCGCAGTATGTTCCGTTATATGGTGTAGATACTGAGG AGGATAGCGTTCCTGAGGTGGAGGAGAACATTGCCACGCGCCAAAGATTAAGCAGGGATC CTACACAATGGTCTTCAGGCATCTGTGCTTGTTTTGATGATCCACAGAGCTGTTGTATTG GTGCGACTTGCCCCTGCTTTCTTTTTGGAAAAAATGCACAGTTCTTGGGATCTGGAACTC TCGCTGGATCATGCACCACCCATTGCATGCTTTGGGGCCTTCTGACAAGTTTCTGCTGTC TGTGTACTGGGGGGCTTGTATTAGCAGTTCCAGGGTCTGCTGTTGCTTGTTATGCTTGTG GATACCGCCAAGCACTAAGAACGAAGTACAACCTTCCGGAAGCACCATGCGGCGATTTGA CGACGCACTTATTTTGCCATCTGTGTGCGATATGCCAAGAGTACAGGGAGATCCGCGAGA GATCAGACAGTAGCGCCTCTTCAGCTCCTGATGTTACTCCACCTCCTGTGCAGACAATGG ATGACCTTTGACTGAGTAGATGACGAGAACATATCCTGCCTGGCAAATCTTTGGTTGGCT TGACATGCCCTTGCCTGTAAGTATTTGTGTTACTGTGCACTGCTCCCACAGCTACGATGT CAGATTTTATGCAGCTGGTGTAAAGATAACCTGTAAACTAATGGACAGCGCGAGAAAATG TAACCCTTTTGTTGCACGATTATAGCATGTAACATTTTTTCTTCATACATGTAGAAATGA AATGGAAACAAAGAGTGTTCTCCTGGACATGAGTTTCTACTTTGGGTGCATATGCACCTG GATGAACAGTAAAATCGAAAACAATAGAATTTTCTTTGAAGTTATG
Protein Sequence (184 aa)
>BART1_0-u19873.005 184 150831_barley_pseudomolecules MVGKGSYVPPQYVPLYGVDTEEDSVPEVEENIATRQRLSRDPTQWSSGICACFDDPQSCC IGATCPCFLFGKNAQFLGSGTLAGSCTTHCMLWGLLTSFCCLCTGGLVLAVPGSAVACYA CGYRQALRTKYNLPEAPCGDLTTHLFCHLCAICQEYREIRERSDSSASSAPDVTPPPVQT MDDL