- Transcript BART1_0-u42531.006
- Transcript IDBART1_0-u42531.006
- Gene IDBART1_0-u42531
Barley RTD
Exon Structure of BART1_0-u42531.006
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22236688 | 22236583 | + |
| chr6H | 2 | 22237825 | 22237685 | + |
| chr6H | 3 | 22239292 | 22238014 | + |
| chr6H | 4 | 22240161 | 22239402 | + |
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 | 0.504037 | 0.834778 | 0 |
| morex | ETI | 0 | 0 | 0 |
| morex | LEA | 1.00079 | 0 | 0.583645 |
| morex | EPI | 0 | 0.84983 | 0 |
| morex | ROO | 0 | 0.45075 | 0.778189 |
| morex | ROO2 | 0.379701 | 0.570853 | 0.660679 |
| morex | NOD | 0.948138 | 0.565704 | 0 |
| morex | RAC | 0.259049 | 0 | 0.163463 |
| morex | INF1 | 1.21964 | 2.00968 | 2.577 |
| morex | INF2 | 1.53687 | 2.63171 | 5.41056 |
| morex | CAR5 | 2.14019 | 3.38436 | 1.81572 |
| morex | CAR15 | 0.679093 | 0 | 0 |
| morex | LEM | 0.184895 | 0 | 0.301862 |
| morex | LOD | 0 | 0 | 0 |
| morex | PAL | 0 | 0 | 0.194406 |
| morex | SEN | 0 | 0.151406 | 0.1885 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03040.2 | +1 | 5e-81 | 261 | 156/185 (84%) | protein|RNA recognition motif containing protein, expressed |
| TAIR PP10 | AT5G52040 @ ARAPORT AT5G52040.4 @ TAIR |
+1 | 8e-45 | 164 | 108/206 (52%) | Symbols: RS41, At-RS41 | RNA-binding (RRM/RBD/RNP motifs) family protein | chr5:21131881-21133318 FORWARD LENGTH=324 |
| BRACH PP3 | Bradi3g02226.1.p | +1 | 6e-88 | 279 | 165/177 (93%) | pacid=32814082 transcript=Bradi3g02226.1 locus=Bradi3g02226 ID=Bradi3g02226.1.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 (2286 bp)
>BART1_0-u42531.006 2286 150831_barley_pseudomolecules CCCTGTCTGTCTCCGTCCTCCCCCCGCTCCACTCGCCGCCGGGTCCGAACCAGCCGCGCC CCCCGTCGAAAACCTAGGGTTCCGCCCTCCCCCGCCCCCTCCGAAGGTTTGGGGAAGATC TGTTTATACAGCAACACCAACATGAGGCCAATTTTCTGCGGGAACCTTGACTATGATGCC CGCCAATCTGAAGTCGAGCGTCTTTTTGGCAAATATGGAAGAGTGGAGCGAGTTGACATG AAGACAGCTCCATACAAGTCTTCCAAGGGAATGGAGTGAATGGTGTGCTCAGTTAGCTTT AACAAGATTGGGTGGGTGCCAAGTGGAAACAGCCGTCCTCGTTGCTGCAAAGACTGCCAT CGCTTCTTCAACCATCCCTGGTGCAGTATGATGCGGTCTGTTATAAGATATGATTGGACA AAGTGTATCAGGCCAGAGACTGTTCAGCAGAATCAGATTATGTTTATTGTTATTTTGTCA AAGTCATTGGACAAGTCCAAACCAGGATATAAATTTAGAAAAAGAAGTTATTTCTTAAAG TTTAGGTCCAGTACTCAATTGTTTCTTTGCCGCAGGAATATCATGAAGCATCTGTGCTCT TCCTGGTTGATGGACTGGGCTCTACCTTTCCTGCCTGAGCCCCTGCCTCATGCCCTGTCC ATTTCCAGGAGTTCACAGTCCACCATGACATCTGTCACTTGGAAACGACCACCTTGTGAC TGATGTCTTACTTTTACATCAATGTTGCACCCTCCTCCCCCGCCCGGTTACACTCTCCCA CGTCGACCAAACCATGCCAATCTCATGGCCGGCTGGAGAAGAGTAGAGGTTCCACCGGCA GCACCACCACCTCTTTTGGTGTACCACGAACGTTTGGATTATCGTACTCTGACATCATTT AGTGCAACATGCAAAAGGTCTGTTCTTATTTGTGCTGACATATCAATTTGTAGCTTCCTG AGGTGATCTTGAAGTTTTTTTTCTCTTGCAAAGATTTTGATCGCCATACAAGCCATTATC TGTTTACCCTAAGGGTTAGTAAAATGTGCGAGCTACTTTAAATAACTAGTCATCTTTCCA TGTTCAACATTGAAGGATTTGCGTTCGTCTACATGGAAGATGAACGTGATGCTGAAGATG CTATCCGTAGACTTGATAGAACTGACTTTGGTAGAACAGGGAGGAGACTGAGAGTCGAAT GGACAAAGGTGCGCAGTTGTAAACTAATAATAAAAGTCATCTCTCAGTAGCCTTATTTTT CTTAATATCCGTCGTCTATTATTTGTGTAGGAGGATCGCAGTGGTGGTCGGAAAGGAAAT GGAAAGAGATCTCCAAGCAGCGTGAAACCAACCAAAACCTTGTTTGTGATCAACTTTGAT CCAATCAACACAAGGACAAGAGATCTGGAGAAGCACTTTGATCTGTATGGCAAGATTGCA AATATCAGAATCAGAAGGAACTTTGCATTTGTCCAGTATGAAACACAGGAGGATGCTACT AAAGCTCTGGACGGTACTAATGGAAGCACTGTGATGGACAGGGTGATTTCTGTTGAGTAT GCGCTTCGTGACGATGATGAAAAAAGGAACGGGTACAGTCCAGACAGGAGAGGAGGCCGT GATAGGTCTCCTGACAGAAGGGACAATCGTGGTAGGTCGGCAAGTCCTTATGGCAGAGGG CGGGAAAGGGGCAGCCCAGACTATGGCAGGGGCAGGGAGAGGGGCAGCCCGGACTATGGC AAGGGCGGTGCCAGAGATAGTCCTGACTATGTCCGTGGTGGAAGCCCGTACGGCGGCAAA GGGGATGACAGGGCTAGCCCCAAGTATGACCGTGAACGCCGTGAAGCCAGTCCTGCCTAT GACAGGCGCCGCAGGTTCGTATGCTGAAAACGCTTCATTATGCTTGCTAAATCGTGTTGA AGCACCACACTGAACATGTTCTCCGCTGTTGTGCAGCCGCTCGCCTGCAAGGGAAGATAG GGACTGAAGCTGTACCATGGATGGCTGCGCTCAATCCTGGGTGCTTCGGACCAAATGGAT GCACCGTCCTAGTGCGATGTTCGCTCAAGTTGGTTATGTTAGGCAGCCAGGAACTTCTGT AATATCTCTCTATTAGCTAGCTCTAGCTGAATGCTTTGTCGATTTAGTTTGAACTGTGAT TGTTAGCTTGAACTTTGTGCAAAGGGATTCTTCCGGTGAGACCATTTGCGGAGCGATGAG ATGTACCGTGTATCGACCGACAGCAGTATTCTAGCTTTGCACTTTGGTTATTCTTCCATA TGTTCC
Protein Sequence (117 aa)
>BART1_0-u42531.006 117 150831_barley_pseudomolecules MDRVISVEYALRDDDEKRNGYSPDRRGGRDRSPDRRDNRGRSASPYGRGRERGSPDYGRG RERGSPDYGKGGARDSPDYVRGGSPYGGKGDDRASPKYDRERREASPAYDRRRRFVC