- Transcript BART1_0-u39718.017
- Transcript IDBART1_0-u39718.017
- Gene IDBART1_0-u39718
Barley RTD
Exon Structure of BART1_0-u39718.017
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 615390084 | 615388833 | - |
| chr5H | 2 | 615390389 | 615390163 | - |
| chr5H | 3 | 615390625 | 615390551 | - |
| chr5H | 4 | 615390934 | 615390818 | - |
| chr5H | 5 | 615392484 | 615392324 | - |
| chr5H | 6 | 615392680 | 615392630 | - |
| chr5H | 7 | 615393173 | 615392820 | - |
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 | 3.3787 | 2.88816 | 2.50655 |
| morex | ETI | 4.0628 | 4.44978 | 3.49739 |
| morex | LEA | 1.59616 | 2.09342 | 2.39798 |
| morex | EPI | 7.8365 | 8.41503 | 6.08924 |
| morex | ROO | 0.668091 | 2.29499 | 0 |
| morex | ROO2 | 1.95395 | 2.36336 | 1.68646 |
| morex | NOD | 1.0974 | 4.32892 | 3.0446 |
| morex | RAC | 4.37014 | 5.18759 | 3.59975 |
| morex | INF1 | 5.55832 | 6.89901 | 7.74964 |
| morex | INF2 | 9.6906 | 11.9832 | 11.4547 |
| morex | CAR5 | 5.17254 | 4.95881 | 4.72304 |
| morex | CAR15 | 4.47546 | 5.15054 | 3.63926 |
| morex | LEM | 2.40048 | 2.93386 | 2.23883 |
| morex | LOD | 5.9519 | 7.08604 | 4.32832 |
| morex | PAL | 3.22317 | 3.75436 | 2.86045 |
| morex | SEN | 2.40817 | 3.40562 | 3.76822 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g35150.1 | +3 | 5e-110 | 332 | 180/242 (74%) | protein|splicing factor U2AF, putative, expressed |
| TAIR PP10 | AT1G10320 @ ARAPORT AT1G10320.1 @ TAIR |
+3 | 4e-69 | 241 | 110/144 (76%) | Symbols: | Zinc finger C-x8-C-x5-C-x3-H type family protein | chr1:3384164-3388373 REVERSE LENGTH=757 |
| BRACH PP3 | Bradi3g45900.1.p | +3 | 1e-159 | 397 | 198/243 (81%) | pacid=32822846 transcript=Bradi3g45900.1 locus=Bradi3g45900 ID=Bradi3g45900.1.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 (2237 bp)
>BART1_0-u39718.017 2237 150831_barley_pseudomolecules TCTCACACCAAGTGGAAGTAACATTTGTTTTTTAAAGGTTGCTAGTCTCACATATGAGTA CAAGTGCACTTGTTTATTTCCGTGGCCCCACATCTGAACTCACCACCAACTCCAATATTT ATAAGTAGGAAAGATAACTGGTTACTTTAATTCTTTTGTAAATTCCCTTCCAAGTGTTAA AATATGCCTGTTGCTTTTTAGAAATTTTGCTTGATCTTCTGGCTACTCTCAGACCTGTGA CATAATGCATGTTCATTGATGCATTCTCCAAGAATTCCCTCTCGAGGCAAGCAGTGACCA ACCACCTAGTTGGTCTCATTTGATTGGAGACGCCCTGAACTTTCATCTGCTACCTACTTG TGAGATGTTCTTGTATTGGACGTGTTGATGATCATTAGGTGACAGGTCATGGAAGTTGCA GTTGAATGGTTGATTTGATCCATAGCTAATAAGTTTTTTATAACATCCTCCAGTTTACAG ACGAAGAGATTGAACAGAGCTATGAAGAATTTTATGAAGACGTGCACACAGAATTTCTGA AATTTGGTGAACTTGTCAACTTCAAGGTATGTAGAAATGGATCGTTCCATCTTCGAGGAA ATGTCTATGTGCATTATAAAGCTTTGGATTCAGCTCTTCTTGCCTACAACAGCATGAATG GTCGATATTTTGCTGGGAAGCAGATAACATGCGAGTTTGTTGCTCTGACGAAATGGAAGT CTGCGATCTGTGGTGAGTACATGAGGTCAAGATTCAAGACATGTTCACATGGAGTTGCTT GTAATTTCATTCATTGCTTTCGTAATCCTGGTGGAGATTATGAGTGGGCTGATTGGGACA ATCCTCCACCTAAATACTGGACTCGGAAGATGGCTGCTCTGTTTGGACCCTCAGATGATG CTGTTTTTGACAAGGCGAGTGATGCCCCAGATTTCGAACGGTTACACAGTTCAGACAGGA AGAGACTGAGAAGTTCTGATGGCAGGTATATTTCAAGTAGACATAGGGATGGAGATGCAC ATAAACGGCACTCATCAAGAGTTTTTTCACATTCGAAGCAAGAACAGAGCAATTATATCA TGAAATATGGGCATACTCGACATAGTAGAGAACCATCTACAGCAAAAAAGCAACGAGGCC ATGAGATTGAAGATGATATTGGCAGATACTGTTCGCCCGTGGAAAATGAAAGAGTGNNNN NNNNNNNNNNNNNNAAAGAGTGTCCCAAACACACAAGCGTGAAGAGAAACATAGAGATGG CCATGGCGATGGAGCACGTGGAGACAATGGTAAAATCAAGTCCAGGAAGCACAGATCTGA ACAGCACGAAAGTCTGGAGTCTGGATGTTCTGATTGGCCTTCAGAATTTGCTGATGCAGG CACGAGCAGAAGTCCTTCATGCAGCAAGTCCACCAACAGGTACAGTAATCACAATAGGAG TCGGGGGCAATCCTTGGATGATTCCAATCTTGAAAGGGGCTACTCCACTGCGGACAAATC ATCAGGGAAAGCGCACATTGCCAAAAGTAGCTCGAGACATTACGTAGAAGATGACTCTTA TGGTGAGAAAGGTAGTGGAAGAGACAAATCTGGAAAGCACAGTGATCATTGTGATGACCC TGATGATAGATGGCTAGCAACAACTAGTGACGTTGATTCAGATGGAGAAACTCAATTCCT GAGATCAAGCAGTGGAATTGGTAAAGGTGGAAAGAATGATAATGCTCCTCGAGACGAGGA TGATCGTTGTCAAAGGTCCAGCAGTAGGTCTGCTAGGTCAAGAGCGAACGAGACGAAGAG CAGTAGGAAGAGGAAGAAGCATCACAGTGAAATCAGGAAGAATAGCGATAGTGATGACAG TCCGTCAGACTCTAGTGACATTAGGGATTCGAGCTCACATGCATGGAGGAGTCGATCAAG AAGCAGTGAGGAAGATCTCTCTTTACACAGACGGAGGAAGGGTCGCCTAGGTCATGATTC GTGATGCTGCTGAAATTTCTGATCATTTGGTCACTAGACTGTCGACTTCGGTTTCTGGAC GATCAAATGTTGTATAGATGCCAGTAGCTTATGCAGCAGTCCTTGCCAGCCTTGCTTTCT TCTTCACTTTGCCGATAAGGTTCTTTTTCCGGATAGAGGTTTCTTGCAAAGCAGAAGGCT TGTAATAGTTTTGCTAATTTAGAGTTGTTTACATCTCACCATTGGTTCCGCCCTGGAATT CCGACTTTTTATGCCCA
Protein Sequence (297 aa)
>BART1_0-u39718.017 297 150831_barley_pseudomolecules MNGRYFAGKQITCEFVALTKWKSAICGEYMRSRFKTCSHGVACNFIHCFRNPGGDYEWAD WDNPPPKYWTRKMAALFGPSDDAVFDKASDAPDFERLHSSDRKRLRSSDGRYISSRHRDG DAHKRHSSRVFSHSKQEQSNYIMKYGHTRHSREPSTAKKQRGHEIEDDIGRYCSPVENER VXXXXXXKECPKHTSVKRNIEMAMAMEHVETMVKSSPGSTDLNSTKVWSLDVLIGLQNLL MQARAEVLHAASPPTGTVITIGVGGNPWMIPILKGATPLRTNHQGKRTLPKVARDIT