- Transcript BART1_0-u18453.006
- Transcript IDBART1_0-u18453.006
- Gene IDBART1_0-u18453
Barley RTD
Exon Structure of BART1_0-u18453.006
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 47557249 | 47557127 | + |
| chr3H | 2 | 47557628 | 47557557 | + |
| chr3H | 3 | 47558732 | 47558504 | + |
| chr3H | 4 | 47559206 | 47559088 | + |
| chr3H | 5 | 47559495 | 47559319 | + |
| chr3H | 6 | 47559849 | 47559802 | + |
| chr3H | 7 | 47560084 | 47560020 | + |
| chr3H | 8 | 47560432 | 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 | 0.257495 | 0 |
| morex | ETI | 0.60446 | 0.661956 | 0.392414 |
| morex | LEA | 0 | 0 | 0 |
| morex | EPI | 0 | 0 | 0 |
| morex | ROO | 0.510542 | 0.390798 | 0 |
| morex | ROO2 | 0 | 0.573358 | 0 |
| morex | NOD | 0.231653 | 0.810418 | 1.56234 |
| morex | RAC | 0 | 0 | 0.291018 |
| morex | INF1 | 0.618853 | 2.56966 | 0.698308 |
| morex | INF2 | 0 | 0 | 0.753128 |
| morex | CAR5 | 1.49846 | 0.664197 | 2.39718 |
| morex | CAR15 | 0.441076 | 0 | 0.243034 |
| morex | LEM | 0.808436 | 0.450248 | 0.497396 |
| morex | LOD | 1.26443 | 0.299922 | 0 |
| morex | PAL | 0.445849 | 0.518315 | 0 |
| morex | SEN | 0 | 0 | 0 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os10g41730.1 | +2 | 3e-95 | 283 | 143/179 (80%) | protein|expressed protein |
| TAIR PP10 | AT5G43822 @ ARAPORT AT5G43822.1 @ TAIR |
+2 | 4e-43 | 148 | 77/180 (43%) | Symbols: | Pentatricopeptide repeat (PPR) superfamily protein | chr5:17620830-17621868 FORWARD LENGTH=195 |
| BRACH PP3 | Bradi3g33790.2.p | +2 | 7e-110 | 319 | 156/179 (87%) | pacid=32818824 transcript=Bradi3g33790.2 locus=Bradi3g33790 ID=Bradi3g33790.2.v3.1 annot-version=v3.1 |
Barley PseudoMolecules GBrowse
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grey: non-coding, green: Barley Morex IBSC 2017 Transcript CDS, red: Barley RTD exons
CDS Sequence (1093 bp)
>BART1_0-u18453.006 1093 150831_barley_pseudomolecules CGGGCCCGCTTGAAATCCCGGTTTTACCCCCGGCCAGCCTCCCTGCTCTTCCTCGAGGCG ACACACCGGTGGACGGCGACGGTGGTAATCGACGGCGGAGGCTCCCTCCCGGCAACAACG ACAACCATTGGAAGCTAGGGTTCATCACTGCACATTGGGGAATTTCGTGTGAAGGACCAC TTCTTCATTCAACATCAGCTGCAGACGTTCCCTAAGAAAATAGGCAAGCACTGCCGAGAA ATCGATCGAGGACCGGGGTTGCTAAGGGAAACGAGATGAGCGGTTGATCGGGATGGAGGT TGTGGTGCGGAAGATGCAGCAGCGGGTGAGGAAGGCACGGGAGGAGACGGAGCGATGGGA TGACCTCAACTCCCGCCTCCTGTCCCAGTTCTCCAATGCTGCCGCCATCATCACCCGCCT TCTGGTACTTGGAGATGCTAAAAATCATGGTATCCTGCGGTGTGTGCCCAACATCAGGGA GGATCTCTTGGGGGCACAGATGAGGAGCCTGGAGCTCATATTTGTTTCAATGAGGGAGAC TCTGGAGGAGTTCAGTGGCATTGCCAAAGGTTTGAGCAAGGTACTGCGCGATGCTAATCA GATGGTGAGGGGTGGATTGGCACTCACTGGGAAACAATTGCAGTTACAAGTGGGAATTTT GCCAACTATTGCAGACTGCTTGGGTGGGCTACAAACACTGTCTGAAATGCACCAGGCTGA GTATGCGCTAAAATCATCAATCATCTCTTTGTTGACATGGAAAAGCAGTTCAAGTGAAAT CGCTGCAATGCGTCAACTCTTGGTAGACCAACCAAACATACCGAAAGATGAAGTGCAATC TGTCTTCGACATTATATTTGCAGATGAAATTTGCTAAGTTGAGCATGCATCCTACTATTG GAAGCCCTATTGCCAAGACATGTTGAAGCAACTGTATTTTGATCTACTCCTTCCGTTCAT AAATATAAGCTTTTCTGACCTTTCTGTGAATCGGATATATATAGACACGTTTTAGTGTCT TTGTTCACTCATTTCACTCGTGTATGTAGTCCATATTGAAATATCCAAACCATGGTATAT TTGTGAACGGAGG
Protein Sequence (194 aa)
>BART1_0-u18453.006 194 150831_barley_pseudomolecules MEVVVRKMQQRVRKAREETERWDDLNSRLLSQFSNAAAIITRLLVLGDAKNHGILRCVPN IREDLLGAQMRSLELIFVSMRETLEEFSGIAKGLSKVLRDANQMVRGGLALTGKQLQLQV GILPTIADCLGGLQTLSEMHQAEYALKSSIISLLTWKSSSSEIAAMRQLLVDQPNIPKDE VQSVFDIIFADEIC