- Transcript BART1_0-u39718.016
- Transcript IDBART1_0-u39718.016
- Gene IDBART1_0-u39718
Barley RTD
Exon Structure of BART1_0-u39718.016
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 615390084 | 615388816 | - |
| chr5H | 2 | 615390389 | 615390163 | - |
| chr5H | 3 | 615390625 | 615390551 | - |
| chr5H | 4 | 615390934 | 615390818 | - |
| chr5H | 5 | 615392416 | 615392324 | - |
| chr5H | 6 | 615392699 | 615392630 | - |
| chr5H | 7 | 615394192 | 615394034 | - |
| chr5H | 8 | 615394470 | 615394336 | - |
| chr5H | 9 | 615394713 | 615394575 | - |
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 | 0.245944 |
| morex | EPI | 0 | 0 | 0 |
| morex | ROO | 0 | 0.152635 | 0.653749 |
| morex | ROO2 | 0 | 0 | 0 |
| morex | NOD | 0 | 0 | 0 |
| morex | RAC | 0 | 0 | 0 |
| morex | INF1 | 0.198721 | 0 | 0 |
| morex | INF2 | 0 | 0.17096 | 0.23025 |
| morex | CAR5 | 0 | 0 | 0.267656 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 0.613913 | 0 | 0 |
| morex | LOD | 0 | 0.151929 | 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_Os02g35150.1 | +3 | 1e-141 | 330 | 165/225 (73%) | protein|splicing factor U2AF, putative, expressed |
| TAIR PP10 | AT1G10320 @ ARAPORT AT1G10320.1 @ TAIR |
+3 | 7e-110 | 239 | 109/143 (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 | 0.0 | 395 | 197/242 (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 (2284 bp)
>BART1_0-u39718.016 2284 150831_barley_pseudomolecules CGAGACAGAAGAAGATGGGGAGTGGGAGTATGTTGAAGATGGACCAGCAGAGATCATATG GCAAGGAAATGAGATCATTGTGAAGAAGAAAAAGGTCAAAATACCAAAGAAGGCAGAGGC TAAACCACTAAGTCAAGAGGAAGAGAGACCTACATCAAATCCGCTGCCACCTCAGTCTGT AGCTGTTGATTCTCAGAGGAGAGAACCTTCCTTGTCTGCTCGAGAACTACTTGAGAAAGT TGCTCAAGAGACTCCAAATTTCGGAACTGAACAGGATAAGGCCCATTGCCCATTTTACCT CAAAACAGCAGCTTGCCGCTTTGGAGTGCGCTGCAGCAGAGTTCACTTCTACCCTGACAA ATCATGCACATTGCTCATGAAAAACATGTATAATGGTCCGGGCCTTGTTTTGGAACAAGA TGAAGGGCTTGAGCTCCTTGACAGTCCAATAGTACTTGTGAGATGTTCTTGTATTGGACG TGTTGATGATCATTAGGTGACAGTTTACAGACGAAGAGATTGAACAGAGCTATGAAGAAT TTTATGAAGACGTGCACACAGAATTTCTGAAATTTGGTGAACTTGTCAACTTCAAGGTAT GTAGAAATGGATCGTTCCATCTTCGAGGAAATGTCTATGTGCATTATAAAGCTTTGGATT CAGCTCTTCTTGCCTACAACAGCATGAATGGTCGATATTTTGCTGGGAAGCAGATAACAT GCGAGTTTGTTGCTCTGACGAAATGGAAGTCTGCGATCTGTGGTGAGTACATGAGGTCAA GATTCAAGACATGTTCACATGGAGTTGCTTGTAATTTCATTCATTGCTTTCGTAATCCTG GTGGAGATTATGAGTGGGCTGATTGGGACAATCCTCCACCTAAATACTGGACTCGGAAGA TGGCTGCTCTGTTTGGACCCTCAGATGATGCTGTTTTTGACAAGGCGAGTGATGCCCCAG ATTTCGAACGGTTACACAGTTCAGACAGGAAGAGACTGAGAAGTTCTGATGGCAGGTATA TTTCAAGTAGACATAGGGATGGAGATGCACATAAACGGCACTCATCAAGAGTTTTTTCAC ATTCGAAGCAAGAACAGAGCAATTATATCATGAAATATGGGCATACTCGACATAGTAGAG AACCATCTACAGCAAAAAAGCAACGAGGCCATGAGATTGAAGATGATATTGGCAGATACT GTTCGCCCGTGGAAAATGAAAGAGTGNNNNNNNNNNNNNNNNNNAAAGAGTGTCCCAAAC ACACAAGCGTGAAGAGAAACATAGAGATGGCCATGGCGATGGAGCACGTGGAGACAATGG TAAAATCAAGTCCAGGAAGCACAGATCTGAACAGCACGAAAGTCTGGAGTCTGGATGTTC TGATTGGCCTTCAGAATTTGCTGATGCAGGCACGAGCAGAAGTCCTTCATGCAGCAAGTC CACCAACAGGTACAGTAATCACAATAGGAGTCGGGGGCAATCCTTGGATGATTCCAATCT TGAAAGGGGCTACTCCACTGCGGACAAATCATCAGGGAAAGCGCACATTGCCAAAAGTAG CTCGAGACATTACGTAGAAGATGACTCTTATGGTGAGAAAGGTAGTGGAAGAGACAAATC TGGAAAGCACAGTGATCATTGTGATGACCCTGATGATAGATGGCTAGCAACAACTAGTGA CGTTGATTCAGATGGAGAAACTCAATTCCTGAGATCAAGCAGTGGAATTGGTAAAGGTGG AAAGAATGATAATGCTCCTCGAGACGAGGATGATCGTTGTCAAAGGTCCAGCAGTAGGTC TGCTAGGTCAAGAGCGAACGAGACGAAGAGCAGTAGGAAGAGGAAGAAGCATCACAGTGA AATCAGGAAGAATAGCGATAGTGATGACAGTCCGTCAGACTCTAGTGACATTAGGGATTC GAGCTCACATGCATGGAGGAGTCGATCAAGAAGCAGTGAGGAAGATCTCTCTTTACACAG ACGGAGGAAGGGTCGCCTAGGTCATGATTCGTGATGCTGCTGAAATTTCTGATCATTTGG TCACTAGACTGTCGACTTCGGTTTCTGGACGATCAAATGTTGTATAGATGCCAGTAGCTT ATGCAGCAGTCCTTGCCAGCCTTGCTTTCTTCTTCACTTTGCCGATAAGGTTCTTTTTCC GGATAGAGGTTTCTTGCAAAGCAGAAGGCTTGTAATAGTTTTGCTAATTTAGAGTTGTTT ACATCTCACCATTGGTTCCGCCCTGGAATTCCGACTTTTTATGCCCATCACACTTGGTAG TAAG
Protein Sequence (297 aa)
>BART1_0-u39718.016 297 150831_barley_pseudomolecules MNGRYFAGKQITCEFVALTKWKSAICGEYMRSRFKTCSHGVACNFIHCFRNPGGDYEWAD WDNPPPKYWTRKMAALFGPSDDAVFDKASDAPDFERLHSSDRKRLRSSDGRYISSRHRDG DAHKRHSSRVFSHSKQEQSNYIMKYGHTRHSREPSTAKKQRGHEIEDDIGRYCSPVENER VXXXXXXKECPKHTSVKRNIEMAMAMEHVETMVKSSPGSTDLNSTKVWSLDVLIGLQNLL MQARAEVLHAASPPTGTVITIGVGGNPWMIPILKGATPLRTNHQGKRTLPKVARDIT