- Transcript BART1_0-u39718.004
- Transcript IDBART1_0-u39718.004
- Gene IDBART1_0-u39718
Barley RTD
Exon Structure of BART1_0-u39718.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 615390084 | 615388573 | - |
| chr5H | 2 | 615390389 | 615390163 | - |
| chr5H | 3 | 615390625 | 615390551 | - |
| chr5H | 4 | 615390934 | 615390818 | - |
| chr5H | 5 | 615392416 | 615392324 | - |
| chr5H | 6 | 615394192 | 615392630 | - |
| chr5H | 7 | 615394470 | 615394336 | - |
| chr5H | 8 | 615394733 | 615394575 | - |
| chr5H | 9 | 615398028 | 615397737 | - |
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 | 0.723423 | 1.74763 | 1.68611 |
| morex | ETI | 0.346119 | 1.21497 | 1.41406 |
| morex | LEA | 1.061 | 1.74685 | 1.44152 |
| morex | EPI | 1.39859 | 1.80067 | 1.27563 |
| morex | ROO | 0 | 0 | 0.37935 |
| morex | ROO2 | 0.508072 | 0.640017 | 0.895858 |
| morex | NOD | 1.17474 | 0.472493 | 1.05638 |
| morex | RAC | 1.86158 | 1.52617 | 1.61333 |
| morex | INF1 | 2.88221 | 3.0255 | 3.63093 |
| morex | INF2 | 6.36657 | 4.45656 | 3.45759 |
| morex | CAR5 | 1.79197 | 2.50979 | 2.30227 |
| morex | CAR15 | 0.329209 | 1.1078 | 1.96967 |
| morex | LEM | 1.12141 | 0.466572 | 0.800427 |
| morex | LOD | 1.25246 | 1.47246 | 1.50627 |
| morex | PAL | 0.299827 | 1.48706 | 0.887465 |
| morex | SEN | 2.08524 | 0.962304 | 2.08853 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os02g35150.1 | +2 | 4e-109 | 330 | 165/225 (73%) | protein|splicing factor U2AF, putative, expressed |
| TAIR PP10 | AT1G10320 @ ARAPORT AT1G10320.1 @ TAIR |
+2 | 4e-66 | 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 | +2 | 9e-159 | 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 (4173 bp)
>BART1_0-u39718.004 4173 150831_barley_pseudomolecules AATCAGTAAGTATTCTGGAGATCAGCAGTAAGTATTCTGGAGATCAGGACACTCACCATC TTCATTCAGTTTTTTCAGGAGCTGCGACTTGGAAGGTAGGGCGTACATTCCAGCACCAAC TGCTTTCCTTATGGCCCAGCCATGGTGAGGAGCAAACACCTGAGCATAAGCCTTTGTCGC TGCGTCCTTCAGGGAGTTGCCTCTGAAACAAAAGAGATCGTGCCCATTCAGATAACATTT ACTCAACAGGCATCTAAGAGTAGCAAACTAAAGGGCTGTCTGACAACATAATTATAACGA TGACCACCGAGACGAGACAGAAGAAGATGGGGAGTGGGAGTATGTTGAAGATGGACCAGC AGAGATCATATGGCAAGGAAATGAGATCATTGTGAAGAAGAAAAAGGTCAAAATACCAAA GAAGGCAGAGGCTAAACCACTAAGTCAAGAGGAAGAGAGACCTACATCAAATCCGCTGCC ACCTCAGTCTGTAGCTGTTGATTCTCAGAGGAGAGAACCTTCCTTGTCTGCTCGAGAACT ACTTGAGAAAGTTGCTCAAGAGACTCCAAATTTCGGAACTGAACAGGATAAGGCCCATTG CCCATTTTACCTCAAAACAGCAGCTTGCCGCTTTGGAGTGCGCTGCAGCAGAGTTCACTT CTACCCTGACAAATCATGCACATTGCTCATGAAAAACATGTATAATGGTCCGGGCCTTGT TTTGGAACAAGATGAAGGGCTTGAGGTTTGTTAGAGGACAATCCCTTGCAAACAAATTCG TATCCTGAACTATTCTGTCTTTTGGCACAACCTTTTAGTATCCTGAACTCATTACAATAC TTATTCCCGACCTACTCATTGTTTTAAGATTATACTCCCTCGCTTTAGGTTTGTTAGGCT CATCTCAAAAAATCTGAATTGTTAGTTTTGGAAGGCCCCTTGCTTTAGGAATAGGCAAAT ATTAAGTACAGCCACATTAATTTCTATCTAAATTTGGTCCTCAATGTGGGGTCAACCAAT GCATGAAGGAGGAGAGTGACCATGCATGCTGCATCAGTACATGGTCCATCACTTAATTAG GTACTCCTTGGTTACAGTGATTTTTTGGATGAGCCAAATGGATTAAGCTTAAACTTTGTG CTGTACAATGAATAACCGTAGGTAGAAACTAGCATAATGCCCGTGCGTTGCTATGAATCC ATAAAAAGACCACTGTCTTAGGAAATCGTCAAAGGATGATGGTGTCTTGGGGTTGTTGCA TGGTTCACGATTGGAAAGAGAGCAAAAATGTAACGAAAGATCGTGTTGCAGTCCTTGAAA AATCAAGCGACCATAGTAGGTACTTTGCAAGATTTATAGTGAGATAACATTTTGAATTTG AAGCATAAGAGGATGGGCATGAGTAAGTTGAATGCACAAGATCGTGAAATTGCAATTTGT TTGCTCTCTTCTGCTATGATATAGAGCTGTAAGAATTGATTGGGCAGAGACTAAAATCGA GACCATGATTTTGAGTTGGAGTTCCATACTTGCATTTACAATTTGCATTTTTGTCAGAGT ATTATTCTCACATTATGGTAGGTGTATTTGTTTACTTGGGATAGGTCTCACACCAAGTGG AAGTAACATTTGTTTTTTAAAGGTTGCTAGTCTCACATATGAGTACAAGTGCACTTGTTT ATTTCCGTGGCCCCACATCTGAACTCACCACCAACTCCAATATTTATAAGTAGGAAAGAT AACTGGTTACTTTAATTCTTTTGTAAATTCCCTTCCAAGTGTTAAAATATGCCTGTTGCT TTTTAGAAATTTTGCTTGATCTTCTGGCTACTCTCAGACCTGTGACATAATGCATGTTCA TTGATGCATTCTCCAAGAATTCCCTCTCGAGGCAAGCAGTGACCAACCACCTAGTTGGTC TCATTTGATTGGAGACGCCCTGAACTTTCATCTGCTACCGTATCCTAAATTTTCATGTTG CTGGTGTTGCTGAGATTTGCTATGTTTTAACTTTTGAAAAGGAAATACCTCCAATGTTTA AAGTTTACAACATTTCTTTGAATATTATTGATGAAGCAGCTCCTTGACAGTCCAATAGTA CTTGTGAGATGTTCTTGTATTGGACGTGTTGATGATCATTAGGTGACAGTTTACAGACGA AGAGATTGAACAGAGCTATGAAGAATTTTATGAAGACGTGCACACAGAATTTCTGAAATT TGGTGAACTTGTCAACTTCAAGGTATGTAGAAATGGATCGTTCCATCTTCGAGGAAATGT CTATGTGCATTATAAAGCTTTGGATTCAGCTCTTCTTGCCTACAACAGCATGAATGGTCG ATATTTTGCTGGGAAGCAGATAACATGCGAGTTTGTTGCTCTGACGAAATGGAAGTCTGC GATCTGTGGTGAGTACATGAGGTCAAGATTCAAGACATGTTCACATGGAGTTGCTTGTAA TTTCATTCATTGCTTTCGTAATCCTGGTGGAGATTATGAGTGGGCTGATTGGGACAATCC TCCACCTAAATACTGGACTCGGAAGATGGCTGCTCTGTTTGGACCCTCAGATGATGCTGT TTTTGACAAGGCGAGTGATGCCCCAGATTTCGAACGGTTACACAGTTCAGACAGGAAGAG ACTGAGAAGTTCTGATGGCAGGTATATTTCAAGTAGACATAGGGATGGAGATGCACATAA ACGGCACTCATCAAGAGTTTTTTCACATTCGAAGCAAGAACAGAGCAATTATATCATGAA ATATGGGCATACTCGACATAGTAGAGAACCATCTACAGCAAAAAAGCAACGAGGCCATGA GATTGAAGATGATATTGGCAGATACTGTTCGCCCGTGGAAAATGAAAGAGTGNNNNNNNN NNNNNNNNNNAAAGAGTGTCCCAAACACACAAGCGTGAAGAGAAACATAGAGATGGCCAT GGCGATGGAGCACGTGGAGACAATGGTAAAATCAAGTCCAGGAAGCACAGATCTGAACAG CACGAAAGTCTGGAGTCTGGATGTTCTGATTGGCCTTCAGAATTTGCTGATGCAGGCACG AGCAGAAGTCCTTCATGCAGCAAGTCCACCAACAGGTACAGTAATCACAATAGGAGTCGG GGGCAATCCTTGGATGATTCCAATCTTGAAAGGGGCTACTCCACTGCGGACAAATCATCA GGGAAAGCGCACATTGCCAAAAGTAGCTCGAGACATTACGTAGAAGATGACTCTTATGGT GAGAAAGGTAGTGGAAGAGACAAATCTGGAAAGCACAGTGATCATTGTGATGACCCTGAT GATAGATGGCTAGCAACAACTAGTGACGTTGATTCAGATGGAGAAACTCAATTCCTGAGA TCAAGCAGTGGAATTGGTAAAGGTGGAAAGAATGATAATGCTCCTCGAGACGAGGATGAT CGTTGTCAAAGGTCCAGCAGTAGGTCTGCTAGGTCAAGAGCGAACGAGACGAAGAGCAGT AGGAAGAGGAAGAAGCATCACAGTGAAATCAGGAAGAATAGCGATAGTGATGACAGTCCG TCAGACTCTAGTGACATTAGGGATTCGAGCTCACATGCATGGAGGAGTCGATCAAGAAGC AGTGAGGAAGATCTCTCTTTACACAGACGGAGGAAGGGTCGCCTAGGTCATGATTCGTGA TGCTGCTGAAATTTCTGATCATTTGGTCACTAGACTGTCGACTTCGGTTTCTGGACGATC AAATGTTGTATAGATGCCAGTAGCTTATGCAGCAGTCCTTGCCAGCCTTGCTTTCTTCTT CACTTTGCCGATAAGGTTCTTTTTCCGGATAGAGGTTTCTTGCAAAGCAGAAGGCTTGTA ATAGTTTTGCTAATTTAGAGTTGTTTACATCTCACCATTGGTTCCGCCCTGGAATTCCGA CTTTTTATGCCCATCACACTTGGTAGTAAGAGCATCTCCAACACATTTTCTGAAGTTACT CCCAATAATTCTGGGTATTGGTACGCTTGCAACTAGTCCCATCACCTAAGCTTAGCTCCC AATAATTTGTGTACATATACCTTGTTTTTTTATTCAAACCCTGCTGTTTCTAGTGCAAAC ATTTCAAATGCATAATATTATTTTTAATTCAAATTCAGGCCATGCACAAGAATTCAAACG GTAGGAGTGCTCCCTCCCTCTCTTCATCATCGC
Protein Sequence (297 aa)
>BART1_0-u39718.004 297 150831_barley_pseudomolecules MNGRYFAGKQITCEFVALTKWKSAICGEYMRSRFKTCSHGVACNFIHCFRNPGGDYEWAD WDNPPPKYWTRKMAALFGPSDDAVFDKASDAPDFERLHSSDRKRLRSSDGRYISSRHRDG DAHKRHSSRVFSHSKQEQSNYIMKYGHTRHSREPSTAKKQRGHEIEDDIGRYCSPVENER VXXXXXXKECPKHTSVKRNIEMAMAMEHVETMVKSSPGSTDLNSTKVWSLDVLIGLQNLL MQARAEVLHAASPPTGTVITIGVGGNPWMIPILKGATPLRTNHQGKRTLPKVARDIT