- Transcript BART1_0-u53404.005
- Transcript IDBART1_0-u53404.005
- Gene IDBART1_0-u53404
Barley RTD
Exon Structure of BART1_0-u53404.005
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr7H | 1 | 387994894 | 387994456 | - |
| chr7H | 2 | 387995344 | 387995023 | - |
| chr7H | 3 | 387996154 | 387996027 | - |
| chr7H | 4 | 387996306 | 387996230 | - |
| chr7H | 5 | 387996488 | 387996426 | - |
| chr7H | 6 | 387996656 | 387996577 | - |
| chr7H | 7 | 387996879 | 387996751 | - |
| chr7H | 8 | 387997091 | 387997003 | - |
| chr7H | 9 | 387997326 | 387997189 | - |
| chr7H | 10 | 387997558 | 387997429 | - |
| chr7H | 11 | 387998007 | 387997921 | - |
| chr7H | 12 | 387998251 | 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 | 2.65725 | 2.42311 | 2.02395 |
| morex | ETI | 3.23605 | 7.17737 | 2.94162 |
| morex | LEA | 3.23127 | 4.13729 | 3.36396 |
| morex | EPI | 2.5104 | 1.78926 | 2.34124 |
| morex | ROO | 0.072889 | 0.509395 | 0.604537 |
| morex | ROO2 | 1.61339 | 0.0838972 | 0 |
| morex | NOD | 4.15828 | 3.24336 | 2.1784 |
| morex | RAC | 2.10418 | 2.31118 | 2.67021 |
| morex | INF1 | 1.72522 | 1.91897 | 0.122785 |
| morex | INF2 | 2.22768 | 2.1472 | 1.38204 |
| morex | CAR5 | 7.65088 | 10.2995 | 8.52029 |
| morex | CAR15 | 0 | 0.992872 | 1.86896 |
| morex | LEM | 5.40657 | 4.70877 | 2.77377 |
| morex | LOD | 4.5514 | 3.33798 | 2.36188 |
| morex | PAL | 1.34699 | 1.51279 | 2.22566 |
| morex | SEN | 2.12712 | 2.16219 | 3.63269 |
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 | 6e-156 | 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 (1838 bp)
>BART1_0-u53404.005 1838 150831_barley_pseudomolecules GCAGGGCCAGCTGCCATATCGTCCTCCGATGTAGGAAGTGCAGCGCGGATGGCGATGGCG GAGGCGGAGGCGGAGGCGGAGGCGGAGGTTCCCGCAGCGTCGCTCTTCGGTGCGGACTGC CGCCTCTGCTCAGCCGACGTGCTCTCGCCCCCCGAGGTTCGGGCAAGGATCGAGGTGGCG GTGCTCAATTTCCTCGCCTTGCTTTCGTCTCCCTCTTCTCCGTCCATCTCCGTCCTCCCC CTGATTTCCCGCAAGTCCACCAACTGCAGCCTGCGCAGCGGCTTGCTGAGTGATGTTTCA TCGGTGTATCTGTCCTACGCCTTCTGCAAGAGGTCGCTAATGAGAGAAAATGATGCCAAG GCATTCGTCAGAGTATGGAAAGTCATGGAGATGTGCTACAAGATCTTGGGCGAAGGGAAG CTTGTCACCCAGCGGGAGTTGTTCTACAAACTACTGTCGGACTCACCCAAGTACTTCAGC TGTCAGCGTCATGTGAATCAAACCATCCAAGATGTTGTTTCATTGCTCCGTTGCACAAGG CAGAGTTTAGGAATCATGGCATCAAGTAGAGGGGCACTGATTGGACGACTTGTGTTGCAT GAACCAGAGGAAGAACACATCGATTGTTCCATTCTCGGACCTTCTGGGCATGCCATTACT GGGGATCTGAACCAATTGAGCAGATTAAATTTGTCTTCAGATGCCCGTTATCTCATTCTA GTGGAGAAGAGGCTGGCTGAAGACCGCTTATATAATCAGCTTCCATGTATCCTGATCACT GCAAAAGGATATCCTGATATCGCAACGAGGTTTATCTTGCATCGACTGAGCCAGACTTTT CCAAATATGCCAATATTTGCATTAGTGGACTGGAACCCTGCAGGGCTCTCTATACTGTGT ACTTACAAATATGGAAGCATATCAATGGGCTTGGAATCATACAGATACGCTTGCAATGTA AAATGGCTTGGCCTAAGAGGAGATGATCTGCAGCTTATCCCTCAGAGTTCATTCCAAGAG TTGAAACCTCGTGATTTGCAGGTCGCCAAAAGCTTGCTGTCATCTAAGTTTCTTCAGGAC ACGCACAGAGCGGAGTTGACACGGATGGTCGAGACGGGCACGCGTGCTGAGATCGAAGCT CTCTATTGCCATGGTTTTGATTTCCTGGGGAAGTTCATCGCCAGGAAGATTGTGCAGGGT GATTACATTTGACAGTGTTTTTTCTCTCTGGCTGTATGGCTCATGATGACGAGGCTACTG GTACAGTAGTGTGAGTGTCTCTGTTAATTGGAGAGCGATATCGCCCATGGCTCATTATGG CTGGTGAGGTCTGAACTTTGACATGCATAGAACAAAACGGATAGTAAAAGTTCTCCCTCT GAGAGTGGAACGATAGCAAGCCTTGGTCGTTCTTTGCTTCCTTTACTTTCTGAGAGAAGG CCACTACAACGATGCCCTGGAAGCAGAGATCCATGTTGTGGCAGCTGGTATGATAATGCG TGGTAGTGACGGGGCGATAGAGGCTGTTTGGATTGAGCCAGGGTCCGCCTCGCCGACCGC GGGCGCGCCAATTTATTGCCGGCCGATTCCGCCGCCCGTGTCTCGCTAACAAATTGGTGC TGGATTGTAGACAGGTAAGGCCAGGGCGCATCAATTACTTCCCCCATTCCTAAATATAAG TTTTTTAAAGGTTTCATTAGGGAATACATACGGATGTATATAAACATGTTAGTGTAGATT TCCTCATTTTGTTTTGTATGTAGTCTTCTAGTGAAATCTTTAAAAAAAAACTTTATATTT AAAAACGAAGAAAGTATTTGATAGCGATTCAAACACGG
Protein Sequence (385 aa)
>BART1_0-u53404.005 385 150831_barley_pseudomolecules MAEAEAEAEAEVPAASLFGADCRLCSADVLSPPEVRARIEVAVLNFLALLSSPSSPSISV LPLISRKSTNCSLRSGLLSDVSSVYLSYAFCKRSLMRENDAKAFVRVWKVMEMCYKILGE GKLVTQRELFYKLLSDSPKYFSCQRHVNQTIQDVVSLLRCTRQSLGIMASSRGALIGRLV LHEPEEEHIDCSILGPSGHAITGDLNQLSRLNLSSDARYLILVEKRLAEDRLYNQLPCIL ITAKGYPDIATRFILHRLSQTFPNMPIFALVDWNPAGLSILCTYKYGSISMGLESYRYAC NVKWLGLRGDDLQLIPQSSFQELKPRDLQVAKSLLSSKFLQDTHRAELTRMVETGTRAEI EALYCHGFDFLGKFIARKIVQGDYI