- Transcript BART1_0-u53404.004
- Transcript IDBART1_0-u53404.004
- Gene IDBART1_0-u53404
Barley RTD
Exon Structure of BART1_0-u53404.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr7H | 1 | 387995344 | 387994362 | - |
| chr7H | 2 | 387996154 | 387996027 | - |
| chr7H | 3 | 387996306 | 387996230 | - |
| chr7H | 4 | 387996488 | 387996426 | - |
| chr7H | 5 | 387996656 | 387996577 | - |
| chr7H | 6 | 387996879 | 387996751 | - |
| chr7H | 7 | 387997091 | 387997003 | - |
| chr7H | 8 | 387997326 | 387997189 | - |
| chr7H | 9 | 387997558 | 387997429 | - |
| chr7H | 10 | 387998007 | 387997921 | - |
| chr7H | 11 | 387998260 | 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 | 0 | 0 |
| morex | ETI | 1.12149 | 0 | 0.147645 |
| morex | LEA | 0.722386 | 0 | 0 |
| morex | EPI | 0.236481 | 0.413077 | 0.673623 |
| morex | ROO | 0 | 0 | 0 |
| morex | ROO2 | 0 | 1.08596 | 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 | 0 |
| morex | CAR15 | 0 | 0 | 0 |
| morex | LEM | 0 | 0 | 0 |
| morex | LOD | 0.781644 | 0 | 0.459761 |
| morex | PAL | 0 | 0 | 0 |
| morex | SEN | 0 | 0 | 0.628841 |
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 | 600 | 317/377 (84%) | protein|OsTOP6A2 - Topoisomerase 6 subunit A homolog 2, expressed |
| TAIR PP10 | AT1G63990 @ ARAPORT AT1G63990.1 @ TAIR |
+1 | 1e-154 | 452 | 233/373 (62%) | Symbols: SPO11-2 | sporulation 11-2 | chr1:23743323-23745351 REVERSE LENGTH=383 |
| BRACH PP3 | Bradi3g16580.1.p | +1 | 0.0 | 648 | 345/376 (92%) | 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 (2069 bp)
>BART1_0-u53404.004 2069 150831_barley_pseudomolecules GAGCCTCTAGCAGGGCCAGCTGCCATATCGTCCTCCGATGTAGGAAGTGCAGCGCGGATG GCGATGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGTTCCCGCAGCGTCGCTCTTCGGT GCGGACTGCCGCCTCTGCTCAGCCGACGTGCTCTCGCCCCCCGAGGTTCGGGCAAGGATC GAGGTGGCGGTGCTCAATTTCCTCGCCTTGCTTTCGTCTCCCTCTTCTCCGTCCATCTCC GTCCTCCCCCTGATTTCCCGCAAGTCCACCAACTGCAGCCTGCGCAGCGGCTTGCTGAGT GATGTTTCATCGGTGTATCTGTCCTACGCCTTCTGCAAGAGGTCGCTAATGAGAGAAAAT GATGCCAAGGCATTCGTCAGAGTATGGAAAGTCATGGAGATGTGCTACAAGATCTTGGGC GAAGGGAAGCTTGTCACCCAGCGGGAGTTGTTCTACAAACTACTGTCGGACTCACCCAAG TACTTCAGCTGTCAGCGTCATGTGAATCAAACCATCCAAGATGTTGTTTCATTGCTCCGT TGCACAAGGCAGAGTTTAGGAATCATGGCATCAAGTAGAGGGGCACTGATTGGACGACTT GTGTTGCATGAACCAGAGGAAGAACACATCGATTGTTCCATTCTCGGACCTTCTGGGCAT GCCATTACTGGGGATCTGAACCAATTGAGCAGATTAAATTTGTCTTCAGATGCCCGTTAT CTCATTCTAGTGGAGAAGAGGCTGGCTGAAGACCGCTTATATAATCAGCTTCCATGTATC CTGATCACTGCAAAAGGATATCCTGATATCGCAACGAGGTTTATCTTGCATCGACTGAGC CAGACTTTTCCAAATATGCCAATATTTGCATTAGTGGACTGGAACCCTGCAGGGCTCTCT ATACTGTGTACTTACAAATATGGAAGCATATCAATGGGCTTGGAATCATACAGATACGCT TGCAATGTAAAATGGCTTGGCCTAAGAGGAGATGATCTGCAGCTTATCCCTCAGAGTTCA TTCCAAGAGTTGAAACCTCGTGATTTGCAGGTCGCCAAAAGCTTGCTGTCATCTAAGTTT CTTCAGGACACGCACAGAGCGGAGTTGACACGGATGGTCGAGACGGGCACGCGTGCTGAG ATCGAAGCTCTCTATTGCCATGGTTTTGATTTCCTGGGGAAGTTCATCGCCAGGAAGATT GTGCAGGGTGATTACATTTGACAGTGTTTTTTCTCTCTGGCTGTATGGCTCATGATGACG AGGCTACTGGTACAGTAGTGTGAGTGTCTCTGTTAATTGGAGAGCGATATCGCCCATGGC TCATTATGGCTGGTGAGGTCTGAACTTTGACATGCATAGAACAAAACGGATAGTAAAAGT TCTCCCTCTGAGAGTGGAACGATAGCAAGTAAGCACGGTTGTACTCCAGTATATTCGTTT AGGCGGTCAGGGTAATTCAGTTTCTGGTGTATGCGTATGCCTTCTGCGCTCCCTGACAGT ACTCTCCCCATAAAATTGGCAATCCAAATGTTGCAGGCCTTGGTCGTTCTTTGCTTCCTT TACTTTCTGAGAGAAGGCCACTACAACGATGCCCTGGAAGCAGAGATCCATGTTGTGGCA GCTGGTATGATAATGCGTGGTAGTGACGGGGCGATAGAGGCTGTTTGGATTGAGCCAGGG TCCGCCTCGCCGACCGCGGGCGCGCCAATTTATTGCCGGCCGATTCCGCCGCCCGTGTCT CGCTAACAAATTGGTGCTGGATTGTAGACAGGTAAGGCCAGGGCGCATCAATTACTTCCC CCATTCCTAAATATAAGTTTTTTAAAGGTTTCATTAGGGAATACATACGGATGTATATAA ACATGTTAGTGTAGATTTCCTCATTTTGTTTTGTATGTAGTCTTCTAGTGAAATCTTTAA AAAAAAACTTTATATTTAAAAACGAAGAAAGTATTTGATAGCGATTCAAACACGGATGAT ATGCATGGTCAACACCAATATTTTGGACGGGCATCTCAAGGCGTCAATCCAAACAGCCCT ATATTTGCAGCCTACGCTTCATCTTCCAC
Protein Sequence (385 aa)
>BART1_0-u53404.004 385 150831_barley_pseudomolecules MAEAEAEAEAEVPAASLFGADCRLCSADVLSPPEVRARIEVAVLNFLALLSSPSSPSISV LPLISRKSTNCSLRSGLLSDVSSVYLSYAFCKRSLMRENDAKAFVRVWKVMEMCYKILGE GKLVTQRELFYKLLSDSPKYFSCQRHVNQTIQDVVSLLRCTRQSLGIMASSRGALIGRLV LHEPEEEHIDCSILGPSGHAITGDLNQLSRLNLSSDARYLILVEKRLAEDRLYNQLPCIL ITAKGYPDIATRFILHRLSQTFPNMPIFALVDWNPAGLSILCTYKYGSISMGLESYRYAC NVKWLGLRGDDLQLIPQSSFQELKPRDLQVAKSLLSSKFLQDTHRAELTRMVETGTRAEI EALYCHGFDFLGKFIARKIVQGDYI