- Transcript BART1_0-u05042.009
- Transcript IDBART1_0-u05042.009
- Gene IDBART1_0-u05042
Barley RTD
Exon Structure of BART1_0-u05042.009
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr1H | 1 | 501617123 | 501616568 | - |
| chr1H | 2 | 501617385 | 501617276 | - |
| chr1H | 3 | 501618080 | 501617967 | - |
| chr1H | 4 | 501618560 | 501618447 | - |
| chr1H | 5 | 501619174 | 501618955 | - |
| chr1H | 6 | 501619750 | 501619330 | - |
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 | 1.17612 | 1.92881 | 3.92492 |
| morex | ETI | 13.8856 | 24.9457 | 13.4937 |
| morex | LEA | 0 | 0 | 6.41861 |
| morex | EPI | 7.42501 | 0.746321 | 1.5621 |
| morex | ROO | 7.65902 | 0 | 0 |
| morex | ROO2 | 2.61925 | 6.96916 | 3.31041 |
| morex | NOD | 8.28863 | 12.8292 | 9.09472 |
| morex | RAC | 9.36158 | 16.2524 | 23.0772 |
| morex | INF1 | 0.00166619 | 1.0057 | 0 |
| morex | INF2 | 0 | 0 | 0.663944 |
| morex | CAR5 | 2.11725 | 0 | 0 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 14.1629 | 13.3212 | 7.09176 |
| morex | LOD | 5.65305 | 4.10221 | 11.1599 |
| morex | PAL | 18.4635 | 5.6092 | 12.3619 |
| morex | SEN | 7.51989 | 1.6569 | 3.07057 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os08g06280.7 | +2 | 3e-60 | 196 | 117/123 (95%) | protein|LSD1 zinc finger domain containing protein, expressed |
| TAIR PP10 | AT1G32540 @ ARAPORT AT1G32540.1 @ TAIR |
+2 | 7e-54 | 180 | 105/122 (86%) | Symbols: LOL1 | lsd one like 1 | chr1:11768253-11769591 FORWARD LENGTH=187 |
| BRACH PP3 | Bradi3g16400.3.p | +2 | 1e-60 | 196 | 118/123 (96%) | pacid=32812785 transcript=Bradi3g16400.3 locus=Bradi3g16400 ID=Bradi3g16400.3.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 (1535 bp)
>BART1_0-u05042.009 1535 150831_barley_pseudomolecules CCAAAACCACATGTTGCTGCACAGGATTGTTGACGGAGATTTCTATAAACGAAAACGAAA GCAAAAAAAATTACACAGAACAGGATAGCGTAGTGAGTTTCGACGGGGCCCACATGGCAT AGGGGATAAGAAAGAGAATCCACGTTCCCAGCCACAGTGCCGTGCTTTACCTTATCTGCC GCATTCCAACTCATGTTGTTATTCTGAGCAAAACTCGACTCGCTCGCTCGTCTCGACATC TGCACCGGATCGAGCTCAGCAAAGCCCGAGCCGGAGGCGCTCGTCTGCCCGGGGAGCGGC GCCATGCGGGTCCGCCTCTTCCTCTGAACCGGGCAAGCGCGAGCCGCCTTCTTCCTCCGG CTCGGCGTCGGCGGCGACGACGAGCGTCGGTGGCGGCATAGCACGGTCCAGCGACGAGCA GAATCGCGGTGTTCTCACCGGAATCTCCCACAATTTATGCAGGATTTCATGTAGAGGAGG GCAATCTGTTCTCATCCCCTCGACTTCCAGCAGAGCGTGCGAAGTCTCGTCCGCAGCAAC GACGACGCCGGCTCAGGCAGCCGCGGGCACGGCAATGCCGGTTCCTCTTGCCCCTTACCC AACTCCTCCTGCGCCCTTCACGCCACCCGCTCCCAATGCAGGGGCTCAAAGCCAACTTGT CTGCTCTGGGTGCCGGAATCTGCTCATGTATCCTGCCGGCGCAACGTCGGTATGCTGCGC GGTTTGCAGTACCGTGACCGCTGTTCCGGCTCCTGGGACCGAGATGGCGCAGCTAGTTTG CGGAGGATGCCACACTCTTCTGATGTACATACGTGGTGCCACAAGTGTACAGTGTTCTTG CTGCCACACTGTCAACCTGGCAATGGAAGCGAATCAGGTTGCGCATGTAAACTGTGGGAG TTGCCGAATGCTGCTCATGTACCAGTACGGCGCAAGGTCCGTCAAATGTGCAGTCTGCAG TTTCGTGACATCAGTTGGGGCATCATCGGGTGCAGAGCAGAAGCCCAGCAACTGAAATCC TGCAAGTTCATTACGAAGGCAGCTTCCCGAAATAAGAATGCTTTGAGTGCACATGTATAG AGTTCTTCCCAGAAGCAACCTTTTCCTCCCCTCTCCATTTCTCCCTTCGTTGGACCTGGC GAGCTTGCGGAATAAACAAGAGTTTTTGGTAATACATAGTTGCTCAAAATTCGTCGAATC ATCTGTGTAACTGGGTCAGACAGATACATGAACCCACCATGTTTATGTTCAAATTTAGCT TCTTTTACTTGTGTTCTATATATTTCAGATTTTTTTTCTTGTGGTCATCGGAAGAATTTC TTCAGATGTGCTTTGCCGTGCGTATTCTTGAACCGATCTATATCACTGCAGACATGATCA TGAACATGAACAGTTTACAAACACAGAAAAGTCCAAATGATGCATGGTTAGGGTGTGCAA ACACATCAGAGCTGATGTTGATTGCAAGGACACAGGATTGGGTGAGTGTGGGGCACCATC TCTCTGATTCTTGCCCAACTCTGAATCTACAGCCG
Protein Sequence (122 aa)
>BART1_0-u05042.009 122 150831_barley_pseudomolecules MLRGLQYRDRCSGSWDRDGAASLRRMPHSSDVHTWCHKCTVFLLPHCQPGNGSESGCACK LWELPNAAHVPVRRKVRQMCSLQFRDISWGIIGCRAEAQQLKSCKFITKAASRNKNALSA HV