- Transcript BART1_0-u05042.013
- Transcript IDBART1_0-u05042.013
- Gene IDBART1_0-u05042
Barley RTD
Exon Structure of BART1_0-u05042.013
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr1H | 1 | 501617123 | 501616762 | - |
| chr1H | 2 | 501617377 | 501617276 | - |
| chr1H | 3 | 501618080 | 501617967 | - |
| chr1H | 4 | 501618560 | 501618447 | - |
| chr1H | 5 | 501619133 | 501618955 | - |
| chr1H | 6 | 501619540 | 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 | 1.34768 | 4.70575 | 5.64374 |
| morex | ETI | 0.00468697 | 8.37416 | 22.2384 |
| morex | LEA | 1.13975 | 0 | 0.495433 |
| morex | EPI | 0.0000000999425 | 8.75083 | 0.000129321 |
| morex | ROO | 3.90635 | 3.88964 | 1.43245 |
| morex | ROO2 | 5.50942 | 6.63423 | 5.2932 |
| morex | NOD | 31.0141 | 38.3604 | 11.39 |
| morex | RAC | 24.8303 | 27.7347 | 42.5619 |
| morex | INF1 | 4.27941 | 0 | 0 |
| morex | INF2 | 0 | 0 | 0 |
| morex | CAR5 | 6.78267 | 10.1381 | 10.116 |
| morex | CAR15 | 0.64053 | 1.1714 | 0 |
| morex | LEM | 24.7882 | 15.2876 | 29.307 |
| morex | LOD | 34.6496 | 29.3818 | 30.7811 |
| morex | PAL | 30.8658 | 31.867 | 39.0221 |
| morex | SEN | 0.622072 | 0 | 4.59935 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os08g06280.7 | +3 | 8e-44 | 110 | 74/74 (100%) | protein|LSD1 zinc finger domain containing protein, expressed |
| TAIR PP10 | AT1G32540 @ ARAPORT AT1G32540.1 @ TAIR |
+3 | 1e-38 | 107 | 69/75 (92%) | Symbols: LOL1 | lsd one like 1 | chr1:11768253-11769591 FORWARD LENGTH=187 |
| BRACH PP3 | Bradi3g16400.3.p | +3 | 5e-44 | 111 | 74/74 (100%) | 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 (1082 bp)
>BART1_0-u05042.013 1082 150831_barley_pseudomolecules AAACTCGACTCGCTCGCTCGTCTCGACATCTGCACCGGATCGAGCTCAGCAAAGCCCGAG CCGGAGGCGCTCGTCTGCCCGGGGAGCGGCGCCATGCGGGTCCGCCTCTTCCTCTGAACC GGGCAAGCGCGAGCCGCCTTCTTCCTCCGGCTCGGCGTCGGCGGCGACGACGAGCGTCGG TGGCGGCATAGCACGGTCCAGCGACGAGCAGGATTTCATGTAGAGGAGGGCAATCTGTTC TCATCCCCTCGACTTCCAGCAGAGCGTGCGAAGTCTCGTCCGCAGCAACGACGACGCCGG CTCAGGCAGCCGCGGGCACGGCAATGCCGGTTCCTCTTGCCCCTTACCCAACTCCTCCTG CGCCCTTCACGCCACCCGCTCCCAATGCAGGGGCTCAAAGCCAACTTGTCTGCTCTGGGT GCCGGAATCTGCTCATGTATCCTGCCGGCGCAACGTCGGTATGCTGCGCGGTTTGCAGTA CCGTGACCGCTGTTCCGGCTCCTGGGACCGAGATGGCGCAGCTAGTTTGCGGAGGATGCC ACACTCTTCTGATGTACATACGTGGTGCCACAAGTGTACAGTGTTCTTGCTGCCACACTG TCAACCTGGCAATGGAAGGTTGCGCATGTAAACTGTGGGAGTTGCCGAATGCTGCTCATG TACCAGTACGGCGCAAGGTCCGTCAAATGTGCAGTCTGCAGTTTCGTGACATCAGTTGGG GCATCATCGGGTGCAGAGCAGAAGCCCAGCAACTGAAATCCTGCAAGTTCATTACGAAGG CAGCTTCCCGAAATAAGAATGCTTTGAGTGCACATGTATAGAGTTCTTCCCAGAAGCAAC CTTTTCCTCCCCTCTCCATTTCTCCCTTCGTTGGACCTGGCGAGCTTGCGGAATAAACAA GAGTTTTTGGTAATACATAGTTGCTCAAAATTCGTCGAATCATCTGTGTAACTGGGTCAG ACAGATACATGAACCCACCATGTTTATGTTCAAATTTAGCTTCTTTTACTTGTGTTCTAT ATATTTCAGATTTTTTTTCTTGTGGTCATCGGAAGAATTTCTTCAGATGTGCTTTGCCGT GC
Protein Sequence (165 aa)
>BART1_0-u05042.013 165 150831_barley_pseudomolecules MPVPLAPYPTPPAPFTPPAPNAGAQSQLVCSGCRNLLMYPAGATSVCCAVCSTVTAVPAP GTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEGCACKLWELPNAAHVPVRRKVR QMCSLQFRDISWGIIGCRAEAQQLKSCKFITKAASRNKNALSAHV