- Transcript BART1_0-u18453.004
- Transcript IDBART1_0-u18453.004
- Gene IDBART1_0-u18453
Barley RTD
Exon Structure of BART1_0-u18453.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 47557249 | 47557123 | + |
| chr3H | 2 | 47558732 | 47558504 | + |
| chr3H | 3 | 47559206 | 47559088 | + |
| chr3H | 4 | 47559495 | 47559319 | + |
| chr3H | 5 | 47559849 | 47559802 | + |
| chr3H | 6 | 47560084 | 47560020 | + |
| chr3H | 7 | 47560431 | 47560173 | + |
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 | 0.842471 | 1.7052 | 1.52556 |
| morex | ETI | 0.910388 | 0 | 0.270007 |
| morex | LEA | 0 | 0.208152 | 0 |
| morex | EPI | 0 | 1.05889 | 0 |
| morex | ROO | 0.249332 | 0.450265 | 0.778082 |
| morex | ROO2 | 1.50784 | 1.35992 | 1.63483 |
| morex | NOD | 1.27355 | 0 | 0 |
| morex | RAC | 0.255679 | 1.87378 | 1.83815 |
| morex | INF1 | 2.03653 | 2.02208 | 1.03599 |
| morex | INF2 | 1.84623 | 2.36292 | 0.713937 |
| morex | CAR5 | 1.83292 | 2.47155 | 2.83236 |
| morex | CAR15 | 0 | 0 | 0.587958 |
| morex | LEM | 0.635616 | 0.28197 | 0.709423 |
| morex | LOD | 0 | 2.98135 | 2.69386 |
| morex | PAL | 0 | 0 | 0.648872 |
| morex | SEN | 0 | 1.22331 | 0.388553 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os10g41730.1 | +3 | 1e-95 | 283 | 143/179 (80%) | protein|expressed protein |
| TAIR PP10 | AT5G43822 @ ARAPORT AT5G43822.1 @ TAIR |
+3 | 2e-43 | 148 | 77/180 (43%) | Symbols: | Pentatricopeptide repeat (PPR) superfamily protein | chr5:17620830-17621868 FORWARD LENGTH=195 |
| BRACH PP3 | Bradi3g33790.2.p | +3 | 3e-110 | 319 | 156/179 (87%) | pacid=32818824 transcript=Bradi3g33790.2 locus=Bradi3g33790 ID=Bradi3g33790.2.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 (1024 bp)
>BART1_0-u18453.004 1024 150831_barley_pseudomolecules AGGTCGGGCCCGCTTGAAATCCCGGTTTTACCCCCGGCCAGCCTCCCTGCTCTTCCTCGA GGCGACACACCGGTGGACGGCGACGGTGGTAATCGACGGCGGAGGCTCCCTCCCGGCAAC AACGACACAGCTGCAGACGTTCCCTAAGAAAATAGGCAAGCACTGCCGAGAAATCGATCG AGGACCGGGGTTGCTAAGGGAAACGAGATGAGCGGTTGATCGGGATGGAGGTTGTGGTGC GGAAGATGCAGCAGCGGGTGAGGAAGGCACGGGAGGAGACGGAGCGATGGGATGACCTCA ACTCCCGCCTCCTGTCCCAGTTCTCCAATGCTGCCGCCATCATCACCCGCCTTCTGGTAC TTGGAGATGCTAAAAATCATGGTATCCTGCGGTGTGTGCCCAACATCAGGGAGGATCTCT TGGGGGCACAGATGAGGAGCCTGGAGCTCATATTTGTTTCAATGAGGGAGACTCTGGAGG AGTTCAGTGGCATTGCCAAAGGTTTGAGCAAGGTACTGCGCGATGCTAATCAGATGGTGA GGGGTGGATTGGCACTCACTGGGAAACAATTGCAGTTACAAGTGGGAATTTTGCCAACTA TTGCAGACTGCTTGGGTGGGCTACAAACACTGTCTGAAATGCACCAGGCTGAGTATGCGC TAAAATCATCAATCATCTCTTTGTTGACATGGAAAAGCAGTTCAAGTGAAATCGCTGCAA TGCGTCAACTCTTGGTAGACCAACCAAACATACCGAAAGATGAAGTGCAATCTGTCTTCG ACATTATATTTGCAGATGAAATTTGCTAAGTTGAGCATGCATCCTACTATTGGAAGCCCT ATTGCCAAGACATGTTGAAGCAACTGTATTTTGATCTACTCCTTCCGTTCATAAATATAA GCTTTTCTGACCTTTCTGTGAATCGGATATATATAGACACGTTTTAGTGTCTTTGTTCAC TCATTTCACTCGTGTATGTAGTCCATATTGAAATATCCAAACCATGGTATATTTGTGAAC GGAG
Protein Sequence (194 aa)
>BART1_0-u18453.004 194 150831_barley_pseudomolecules MEVVVRKMQQRVRKAREETERWDDLNSRLLSQFSNAAAIITRLLVLGDAKNHGILRCVPN IREDLLGAQMRSLELIFVSMRETLEEFSGIAKGLSKVLRDANQMVRGGLALTGKQLQLQV GILPTIADCLGGLQTLSEMHQAEYALKSSIISLLTWKSSSSEIAAMRQLLVDQPNIPKDE VQSVFDIIFADEIC