- Transcript BART1_0-u53404.003
- Transcript IDBART1_0-u53404.003
- Gene IDBART1_0-u53404
Barley RTD
Exon Structure of BART1_0-u53404.003
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr7H | 1 | 387994410 | 387993893 | - |
| chr7H | 2 | 387994894 | 387994660 | - |
| chr7H | 3 | 387995344 | 387995023 | - |
| chr7H | 4 | 387996154 | 387996027 | - |
| chr7H | 5 | 387996306 | 387996230 | - |
| chr7H | 6 | 387996488 | 387996426 | - |
| chr7H | 7 | 387996671 | 387996577 | - |
| chr7H | 8 | 387996879 | 387996751 | - |
| chr7H | 9 | 387997091 | 387997003 | - |
| chr7H | 10 | 387997326 | 387997189 | - |
| chr7H | 11 | 387997558 | 387997429 | - |
| chr7H | 12 | 387998007 | 387997921 | - |
| chr7H | 13 | 387998269 | 387998096 | - |
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 | 0.430464 | 0.329154 | 0.202786 |
| morex | ETI | 0 | 0.249043 | 0 |
| morex | LEA | 0 | 0.68595 | 0 |
| morex | EPI | 0.511649 | 1.09416 | 0.288156 |
| morex | ROO | 0 | 0.00011997 | 0.2741 |
| morex | ROO2 | 0 | 0 | 0 |
| morex | NOD | 0.263377 | 0.208057 | 0 |
| morex | RAC | 0 | 0.224408 | 0 |
| morex | INF1 | 0 | 0.226343 | 0.378308 |
| morex | INF2 | 0.293321 | 0.411111 | 1.41474 |
| morex | CAR5 | 1.22762 | 0.000665127 | 2.59085 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 0.338836 | 0 | 0.176621 |
| morex | LOD | 0 | 0 | 0 |
| morex | PAL | 0 | 0 | 0.193161 |
| morex | SEN | 0.782841 | 0 | 0.193623 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os08g06050.1 | +1 | 0.0 | 617 | 322/377 (85%) | protein|OsTOP6A2 - Topoisomerase 6 subunit A homolog 2, expressed |
| TAIR PP10 | AT1G63990 @ ARAPORT AT1G63990.1 @ TAIR |
+1 | 1e-158 | 464 | 236/373 (63%) | Symbols: SPO11-2 | sporulation 11-2 | chr1:23743323-23745351 REVERSE LENGTH=383 |
| BRACH PP3 | Bradi3g16580.1.p | +1 | 0.0 | 664 | 349/376 (93%) | pacid=32817968 transcript=Bradi3g16580.1 locus=Bradi3g16580 ID=Bradi3g16580.1.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 (2185 bp)
>BART1_0-u53404.003 2185 150831_barley_pseudomolecules CCAGCATAAGAGCCTCTAGCAGGGCCAGCTGCCATATCGTCCTCCGATGTAGGAAGTGCA GCGCGGATGGCGATGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGTTCCCGCAGCGTCG CTCTTCGGTGCGGACTGCCGCCTCTGCTCAGCCGACGTGCTCTCGCCCCCCGAGGTTCGG GCAAGGATCGAGGTGGCGGTGCTCAATTTCCTCGCCTTGCTTTCGTCTCCCTCTTCTCCG TCCATCTCCGTCCTCCCCCTGATTTCCCGCAAGTCCACCAACTGCAGCCTGCGCAGCGGC TTGCTGAGTGATGTTTCATCGGTGTATCTGTCCTACGCCTTCTGCAAGAGGTCGCTAATG AGAGAAAATGATGCCAAGGCATTCGTCAGAGTATGGAAAGTCATGGAGATGTGCTACAAG ATCTTGGGCGAAGGGAAGCTTGTCACCCAGCGGGAGTTGTTCTACAAACTACTGTCGGAC TCACCCAAGTACTTCAGCTGTCAGCGTCATGTGAATCAAACCATCCAAGATGTTGTTTCA TTGCTCCGTTGCACAAGGCAGAGTTTAGGAATCATGGCATCAAGTAGAGGGGCACTGATT GGACGACTTGTGTTGCATGAACCAGAGGAAGAACACATCGATTGTTCCATTCTCGGACCT TCTGGGCATGCCATTACTGGGGATCTGAACCAATTGAGCAGATTAAATTTGTCTTCAGAT GCCCGTTATCTCATTCTAGTGGAGAAGGATGCCATATTTCAGAGGCTGGCTGAAGACCGC TTATATAATCAGCTTCCATGTATCCTGATCACTGCAAAAGGATATCCTGATATCGCAACG AGGTTTATCTTGCATCGACTGAGCCAGACTTTTCCAAATATGCCAATATTTGCATTAGTG GACTGGAACCCTGCAGGGCTCTCTATACTGTGTACTTACAAATATGGAAGCATATCAATG GGCTTGGAATCATACAGATACGCTTGCAATGTAAAATGGCTTGGCCTAAGAGGAGATGAT CTGCAGCTTATCCCTCAGAGTTCATTCCAAGAGTTGAAACCTCGTGATTTGCAGGTCGCC AAAAGCTTGCTGTCATCTAAGTTTCTTCAGGACACGCACAGAGCGGAGTTGACACGGATG GTCGAGACGGGCACGCGTGCTGAGATCGAAGCTCTCTATTGCCATGGTTTTGATTTCCTG GGGAAGTTCATCGCCAGGAAGATTGTGCAGGGTGATTACATTTGACAGTGTTTTTTCTCT CTGGCTGTATGGCTCATGATGACGAGGCTACTGGTACAGTAGTGTGAGTGTCTCTGTTAA TTGGAGAGCGATATCGCCCATGGCTCATTATGGCTGGTGAGGTCTGAACTTTGACATGCA TAGAACAAAACGGATAGTAAAAGTTCTCCCTCTGAGAGTGGAACGATAGCAAGCCTTGGT CGTTCTTTGCTTCCTTTACTTTCTGAGAGAAGGCCACTACAACGATGCCCTGGAAGCAGA GATCCATGTTGTGGCAGCTGGTATGATAATGCGTGGTAGTGACGGGGCGATAGAGGCTGT TTGGATTGAGCCAGGGTCCGCCTCGCCGACCGCGGGCGCGCCAATTTATTGCCGGCCGAT TCCGCCGCCCGTGTCTCGCTAACAAATTGGTGCTGGATTGTAGACAGGCGTCAATCCAAA CAGCCCTATATTTGCAGCCTACGCTTCATCTTCCACTACAACGATGCCCTCGAAGCAGAG ATCCATGTTTTGCAAGGTATGGTTTTTTCCATCAACATACTGCTCTGGTCATTGTCCACT AGGATTCTTTTGTCGCTTTGAAGACCCTGTCTACTTTTGGTGTGGACCTTTCGACATATG AACAACTAGTTTCTGAGAGGGTCATTAGTGAATGATAGGGAGTTTTTGGGATTCGAAGAG AACAAAACAGAGTGGCAGATTCTCTAACAAACTACAGTCGCATGAAGCGTACCACGAGAG TGTAGCTTAACCCTAGTCCCCCATATATTGAAGAACATGTGCCTCTTGACTGAAACTCTA TAAACTTGGATGAAACTTCTATTACCCCGGGAAAAGAATCATAAAACCTGAATCCTCGGC ATCACGGTAGTAAGTGTAGTCGTTCTCCAACATCCATCAGAAGTTAGACAGGCCCTAGTG GCTGCTGCGTATGCGAGGCTATGAC
Protein Sequence (392 aa)
>BART1_0-u53404.003 392 150831_barley_pseudomolecules MAMAEAEAEAEAEVPAASLFGADCRLCSADVLSPPEVRARIEVAVLNFLALLSSPSSPSI SVLPLISRKSTNCSLRSGLLSDVSSVYLSYAFCKRSLMRENDAKAFVRVWKVMEMCYKIL GEGKLVTQRELFYKLLSDSPKYFSCQRHVNQTIQDVVSLLRCTRQSLGIMASSRGALIGR LVLHEPEEEHIDCSILGPSGHAITGDLNQLSRLNLSSDARYLILVEKDAIFQRLAEDRLY NQLPCILITAKGYPDIATRFILHRLSQTFPNMPIFALVDWNPAGLSILCTYKYGSISMGL ESYRYACNVKWLGLRGDDLQLIPQSSFQELKPRDLQVAKSLLSSKFLQDTHRAELTRMVE TGTRAEIEALYCHGFDFLGKFIARKIVQGDYI