- Transcript BART1_0-u42531.003
- Transcript IDBART1_0-u42531.003
- Gene IDBART1_0-u42531
Barley RTD
Exon Structure of BART1_0-u42531.003
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr6H | 1 | 22236688 | 22236577 | + |
| chr6H | 2 | 22239292 | 22237685 | + |
| chr6H | 3 | 22239749 | 22239417 | + |
| chr6H | 4 | 22240194 | 22239832 | + |
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 | 5.47729 | 10.8915 | 12.1927 |
| morex | ETI | 6.86417 | 6.46757 | 6.33579 |
| morex | LEA | 6.92443 | 3.99214 | 5.41831 |
| morex | EPI | 3.83613 | 4.95286 | 4.08038 |
| morex | ROO | 1.23033 | 6.3563 | 3.42808 |
| morex | ROO2 | 6.04629 | 4.99016 | 5.26575 |
| morex | NOD | 4.71636 | 6.76476 | 4.28121 |
| morex | RAC | 9.24402 | 9.22716 | 8.61124 |
| morex | INF1 | 25.0735 | 22.5531 | 25.5522 |
| morex | INF2 | 33.4773 | 31.2872 | 33.5528 |
| morex | CAR5 | 24.1492 | 25.4073 | 22.4232 |
| morex | CAR15 | 9.94458 | 9.88952 | 11.3543 |
| morex | LEM | 4.01511 | 4.53796 | 3.99165 |
| morex | LOD | 6.32632 | 5.19886 | 5.90073 |
| morex | PAL | 4.22536 | 6.23884 | 6.22741 |
| morex | SEN | 6.31069 | 7.28162 | 4.52567 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g03040.3 | +3 | 1e-67 | 225 | 140/171 (82%) | protein|RNA recognition motif containing protein, expressed |
| TAIR PP10 | AT5G52040 @ ARAPORT AT5G52040.4 @ TAIR |
+3 | 5e-39 | 147 | 100/194 (52%) | Symbols: RS41, At-RS41 | RNA-binding (RRM/RBD/RNP motifs) family protein | chr5:21131881-21133318 FORWARD LENGTH=324 |
| BRACH PP3 | Bradi3g02226.1.p | +3 | 9e-78 | 253 | 154/168 (92%) | 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 (2416 bp)
>BART1_0-u42531.003 2416 150831_barley_pseudomolecules ACCTGCCCCTGTCTGTCTCCGTCCTCCCCCCGCTCCACTCGCCGCCGGGTCCGAACCAGC CGCGCCCCCCGTCGAAAACCTAGGGTTCCGCCCTCCCCCGCCCCCTCCGAAGGTTTGGGG AAGATCTGTTTATACAGCAACACCAACATGAGGCCAATTTTCTGCGGGAACCTTGACTAT GATGCCCGCCAATCTGAAGTCGAGCGTCTTTTTGGCAAATATGGAAGAGTGGAGCGAGTT GACATGAAGACAGGTATGAACTCTTTGTGTCCATTCTCTAGATTTAAGTTGTCCTTTTTA CCATCTGATTTTATGTTGCACCTATTTGGTGGTGTCGGTCATTAAGGCAACAAACTCTTC TAAGAAATAAACTTACAAGTGTAATGCTTGAGTAAACTGCTATTTACTCAAAAGGGATAT TAATGTGCACAAATACATTAGCTCCATACAAGTCTTCCAAGGGAATGGAGTGAATGGTGT GCTCAGTTAGCTTTAACAAGATTGGGTGGGTGCCAAGTGGAAACAGCCGTCCTCGTTGCT GCAAAGACTGCCATCGCTTCTTCAACCATCCCTGGTGCAGTATGATGCGGTCTGTTATAA GATATGATTGGACAAAGTGTATCAGGCCAGAGACTGTTCAGCAGAATCAGATTATGTTTA TTGTTATTTTGTCAAAGTCATTGGACAAGTCCAAACCAGGATATAAATTTAGAAAAAGAA GTTATTTCTTAAAGTTTAGGTCCAGTACTCAATTGTTTCTTTGCCGCAGGAATATCATGA AGCATCTGTGCTCTTCCTGGTTGATGGACTGGGCTCTACCTTTCCTGCCTGAGCCCCTGC CTCATGCCCTGTCCATTTCCAGGAGTTCACAGTCCACCATGACATCTGTCACTTGGAAAC GACCACCTTGTGACTGATGTCTTACTTTTACATCAATGTTGCACCCTCCTCCCCCGCCCG GTTACACTCTCCCACGTCGACCAAACCATGCCAATCTCATGGCCGGCTGGAGAAGAGTAG AGGTTCCACCGGCAGCACCACCACCTCTTTTGGTGTACCACGAACGTTTGGATTATCGTA CTCTGACATCATTTAGTGCAACATGCAAAAGGTCTGTTCTTATTTGTGCTGACATATCAA TTTGTAGCTTCCTGAGGTGATCTTGAAGTTTTTTTTCTCTTGCAAAGATTTTGATCGCCA TACAAGCCATTATCTGTTTACCCTAAGGGTTAGTAAAATGTGCGAGCTACTTTAAATAAC TAGTCATCTTTCCATGTTCAACATTGAAGGATTTGCGTTCGTCTACATGGAAGATGAACG TGATGCTGAAGATGCTATCCGTAGACTTGATAGAACTGACTTTGGTAGAACAGGGAGGAG ACTGAGAGTCGAATGGACAAAGGTGCGCAGTTGTAAACTAATAATAAAAGTCATCTCTCA GTAGCCTTATTTTTCTTAATATCCGTCGTCTATTATTTGTGTAGGAGGATCGCAGTGGTG GTCGGAAAGGAAATGGAAAGAGATCTCCAAGCAGCGTGAAACCAACCAAAACCTTGTTTG TGATCAACTTTGATCCAATCAACACAAGGACAAGAGATCTGGAGAAGCACTTTGATCTGT ATGGCAAGATTGCAAATATCAGAATCAGAAGGAACTTTGCATTTGTCCAGTATGAAACAC AGGAGGATGCTACTAAAGCTCTGGACGGTACTAATGGAAGGGTGATTTCTGTTGAGTATG CGCTTCGTGACGATGATGAAAAAAGGAACGGGTACAGTCCAGACAGGAGAGGAGGCCGTG ATAGGTCTCCTGACAGAAGGGACAATCGTGGTAGGTCGGCAAGTCCTTATGGCAGAGGGC GGGAAAGGGGCAGCCCAGACTATGGCAGGGGCAGGGAGAGGGGCAGCCCGGACTATGGCA AGGGCGGTGCCAGAGATAGTCCTGACTATGTCCGTGGTGGAAGCCCGTACGGCGGCAAAG GGGATGACAGGGCTAGCCCCAAGTATGACCGTGAACGCCGTGAAGCCAGTCCTGCCTATG ACAGGCGCCGCAGCCGCTCGCCTGCAAGGGAAGATAGGGACTGAAGCTGTACCATGGATG GCTGCGCTCAATCCTGGGTGCTTCGGACCAAATGGATGCACCGTCCTAGTGCGATGTTCG CTCAAGTTGGTTATGTTAGGCAGCCAGGAACTTCTGTAATATCTCTCTATTAGCTAGCTC TAGCTGAATGCTTTGTCGATTTAGTTTGAACTGTGATTGTTAGCTTGAACTTTGTGCAAA GGGATTCTTCCGGTGAGACCATTTGCGGAGCGATGAGATGTACCGTGTATCGACCGACAG CAGTATTCTAGCTTTGCACTTTGGTTATTCTTCCATATGTTCCTATTCTTCACTATTGTT TCTGCTTGTGTGCTGG
Protein Sequence (114 aa)
>BART1_0-u42531.003 114 150831_barley_pseudomolecules TCPCLSPSSPRSTRRRVRTSRAPRRKPRVPPSPAPSEGLGKICLYSNTNMRPIFCGNLDY DARQSEVERLFGKYGRVERVDMKTGMNSLCPFSRFKLSFLPSDFMLHLFGGVGH