- Transcript BART1_0-u18453.003
- Transcript IDBART1_0-u18453.003
- Gene IDBART1_0-u18453
Barley RTD
Exon Structure of BART1_0-u18453.003
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr3H | 1 | 47557249 | 47557111 | + |
| chr3H | 2 | 47557628 | 47557557 | + |
| chr3H | 3 | 47558732 | 47558463 | + |
| chr3H | 4 | 47559206 | 47559088 | + |
| chr3H | 5 | 47559506 | 47559319 | + |
| chr3H | 6 | 47559849 | 47559802 | + |
| chr3H | 7 | 47560084 | 47560020 | + |
| chr3H | 8 | 47560460 | 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 | 0 |
| morex | ETI | 0 | 0 | 0 |
| morex | LEA | 0 | 0 | 0 |
| morex | EPI | 0 | 0 | 0 |
| morex | ROO | 0 | 0 | 0 |
| morex | ROO2 | 0 | 0 | 0 |
| morex | NOD | 0 | 0 | 0 |
| morex | RAC | 0 | 0 | 0 |
| morex | INF1 | 0 | 0 | 0 |
| morex | INF2 | 0 | 0 | 0 |
| morex | CAR5 | 0 | 0 | 2.85617 |
| morex | CAR15 | 0 | 0 | 1.31159 |
| morex | LEM | 0 | 0 | 0 |
| morex | LOD | 0 | 0 | 0 |
| morex | PAL | 0 | 0 | 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 | 9e-72 | 210 | 98/128 (77%) | protein|expressed protein |
| TAIR PP10 | AT5G43822 @ ARAPORT AT5G43822.1 @ TAIR |
+2 | 2e-31 | 91 | 47/128 (37%) | Symbols: | Pentatricopeptide repeat (PPR) superfamily protein | chr5:17620830-17621868 FORWARD LENGTH=195 |
| BRACH PP3 | Bradi3g33790.2.p | +2 | 9e-83 | 225 | 109/128 (85%) | 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 (1189 bp)
>BART1_0-u18453.003 1189 150831_barley_pseudomolecules TTGCCCTCTTACAGGTCGGGCCCGCTTGAAATCCCGGTTTTACCCCCGGCCAGCCTCCCT GCTCTTCCTCGAGGCGACACACCGGTGGACGGCGACGGTGGTAATCGACGGCGGAGGCTC CCTCCCGGCAACAACGACAACCATTGGAAGCTAGGGTTCATCACTGCACATTGGGGAATT TCGTGTGAAGGACCACTTCTTCATTCAACATGTTGACCTGAGCCCAGCCTATCATACGTG CCTCGTTCTCAGCAGCTGCAGACGTTCCCTAAGAAAATAGGCAAGCACTGCCGAGAAATC GATCGAGGACCGGGGTTGCTAAGGGAAACGAGATGAGCGGTTGATCGGGATGGAGGTTGT GGTGCGGAAGATGCAGCAGCGGGTGAGGAAGGCACGGGAGGAGACGGAGCGATGGGATGA CCTCAACTCCCGCCTCCTGTCCCAGTTCTCCAATGCTGCCGCCATCATCACCCGCCTTCT GGTACTTGGAGATGCTAAAAATCATGGTATCCTGCGGTGTGTGCCCAACATCAGGGAGGA TCTCTTGGGGGCACAGATGAGGAGCCTGGAGCTCATATTTGTTTCAATGAGGGAGACTCT GGAGGAGTTCAGTGGCATTGCCAAAGGTTTGAGCAAGGTACTGCGCGATGCTAATCAGAT GGTGAGGGGTGGATTGGCACTCACTGGGAAACAATTGCAGTTACAAGTGGGAATTTTGCC AACTATTGCAGACTGCTTGGGTGGGCTACAAACACTGTCTGAAATGCACCAGGCTGAGTA CGAAACAAGTATGCGCTAAAATCATCAATCATCTCTTTGTTGACATGGAAAAGCAGTTCA AGTGAAATCGCTGCAATGCGTCAACTCTTGGTAGACCAACCAAACATACCGAAAGATGAA GTGCAATCTGTCTTCGACATTATATTTGCAGATGAAATTTGCTAAGTTGAGCATGCATCC TACTATTGGAAGCCCTATTGCCAAGACATGTTGAAGCAACTGTATTTTGATCTACTCCTT CCGTTCATAAATATAAGCTTTTCTGACCTTTCTGTGAATCGGATATATATAGACACGTTT TAGTGTCTTTGTTCACTCATTTCACTCGTGTATGTAGTCCATATTGAAATATCCAAACCA TGGTATATTTGTGAACGGAGGGAGTACTTTCTTATCTGAACAAAGTGTT
Protein Sequence (149 aa)
>BART1_0-u18453.003 149 150831_barley_pseudomolecules MEVVVRKMQQRVRKAREETERWDDLNSRLLSQFSNAAAIITRLLVLGDAKNHGILRCVPN IREDLLGAQMRSLELIFVSMRETLEEFSGIAKGLSKVLRDANQMVRGGLALTGKQLQLQV GILPTIADCLGGLQTLSEMHQAEYETSMR