- Transcript BART1_0-u53404.006
- Transcript IDBART1_0-u53404.006
- Gene IDBART1_0-u53404
Barley RTD
Exon Structure of BART1_0-u53404.006
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr7H | 1 | 387995344 | 387994485 | - |
| chr7H | 2 | 387996154 | 387996027 | - |
| chr7H | 3 | 387996306 | 387996230 | - |
| chr7H | 4 | 387996488 | 387996426 | - |
| chr7H | 5 | 387996671 | 387996577 | - |
| chr7H | 6 | 387996879 | 387996751 | - |
| chr7H | 7 | 387997091 | 387997003 | - |
| chr7H | 8 | 387997326 | 387997189 | - |
| chr7H | 9 | 387997558 | 387997429 | - |
| chr7H | 10 | 387998007 | 387997921 | - |
| chr7H | 11 | 387998207 | 387998092 | - |
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 | 0.364159 | 0 | 0.665046 |
| morex | ETI | 9.83229 | 3.82418 | 6.87678 |
| morex | LEA | 0 | 0 | 2.05501 |
| morex | EPI | 0.000000788535 | 4.35152 | 0.836612 |
| morex | ROO | 1.28186 | 0.605019 | 0 |
| morex | ROO2 | 0.947872 | 2.01969 | 1.85034 |
| morex | NOD | 0 | 1.42857 | 2.54392 |
| morex | RAC | 2.20387 | 3.42111 | 3.43098 |
| morex | INF1 | 0 | 0 | 0 |
| morex | INF2 | 0.199735 | 0 | 0 |
| morex | CAR5 | 0 | 2.26298 | 0 |
| morex | CAR15 | 0.299174 | 0.211652 | 0.193523 |
| morex | LEM | 4.51045 | 3.14205 | 4.28961 |
| morex | LOD | 5.71845 | 2.95897 | 3.50961 |
| morex | PAL | 2.26548 | 4.42193 | 3.83068 |
| morex | SEN | 5.82923 | 4.64236 | 0.877976 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os08g06050.1 | +3 | 0.0 | 593 | 309/362 (85%) | protein|OsTOP6A2 - Topoisomerase 6 subunit A homolog 2, expressed |
| TAIR PP10 | AT1G63990 @ ARAPORT AT1G63990.1 @ TAIR |
+3 | 5e-156 | 454 | 229/359 (64%) | Symbols: SPO11-2 | sporulation 11-2 | chr1:23743323-23745351 REVERSE LENGTH=383 |
| BRACH PP3 | Bradi3g16580.1.p | +3 | 0.0 | 631 | 332/360 (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 (1912 bp)
>BART1_0-u53404.006 1912 150831_barley_pseudomolecules GCGGATGGCGATGGCGGAGGCGGAGGCGGAGGCGGAGGCGGAGGTTCCCGCAGCGTCGCT CTTCGGTGCGGACTGCCGCCTCTGCTCAGCCGACGTGCTCTCGCCCCCCGAGGTCTGTTC GGGCAAGGATCGAGGTGGCGGTGCTCAATTTCCTCGCCTTGCTTTCGTCTCCCTCTTCTC CGTCCATCTCCGTCCTCCCCCTGATTTCCCGCAAGTCCACCAACTGCAGCCTGCGCAGCG GCTTGCTGAGTGATGTTTCATCGGTGTATCTGTCCTACGCCTTCTGCAAGAGGTCGCTAA TGAGAGAAAATGATGCCAAGGCATTCGTCAGAGTATGGAAAGTCATGGAGATGTGCTACA AGATCTTGGGCGAAGGGAAGCTTGTCACCCAGCGGGAGTTGTTCTACAAACTACTGTCGG ACTCACCCAAGTACTTCAGCTGTCAGCGTCATGTGAATCAAACCATCCAAGATGTTGTTT CATTGCTCCGTTGCACAAGGCAGAGTTTAGGAATCATGGCATCAAGTAGAGGGGCACTGA TTGGACGACTTGTGTTGCATGAACCAGAGGAAGAACACATCGATTGTTCCATTCTCGGAC CTTCTGGGCATGCCATTACTGGGGATCTGAACCAATTGAGCAGATTAAATTTGTCTTCAG ATGCCCGTTATCTCATTCTAGTGGAGAAGGATGCCATATTTCAGAGGCTGGCTGAAGACC GCTTATATAATCAGCTTCCATGTATCCTGATCACTGCAAAAGGATATCCTGATATCGCAA CGAGGTTTATCTTGCATCGACTGAGCCAGACTTTTCCAAATATGCCAATATTTGCATTAG TGGACTGGAACCCTGCAGGGCTCTCTATACTGTGTACTTACAAATATGGAAGCATATCAA TGGGCTTGGAATCATACAGATACGCTTGCAATGTAAAATGGCTTGGCCTAAGAGGAGATG ATCTGCAGCTTATCCCTCAGAGTTCATTCCAAGAGTTGAAACCTCGTGATTTGCAGGTCG CCAAAAGCTTGCTGTCATCTAAGTTTCTTCAGGACACGCACAGAGCGGAGTTGACACGGA TGGTCGAGACGGGCACGCGTGCTGAGATCGAAGCTCTCTATTGCCATGGTTTTGATTTCC TGGGGAAGTTCATCGCCAGGAAGATTGTGCAGGGTGATTACATTTGACAGTGTTTTTTCT CTCTGGCTGTATGGCTCATGATGACGAGGCTACTGGTACAGTAGTGTGAGTGTCTCTGTT AATTGGAGAGCGATATCGCCCATGGCTCATTATGGCTGGTGAGGTCTGAACTTTGACATG CATAGAACAAAACGGATAGTAAAAGTTCTCCCTCTGAGAGTGGAACGATAGCAAGTAAGC ACGGTTGTACTCCAGTATATTCGTTTAGGCGGTCAGGGTAATTCAGTTTCTGGTGTATGC GTATGCCTTCTGCGCTCCCTGACAGTACTCTCCCCATAAAATTGGCAATCCAAATGTTGC AGGCCTTGGTCGTTCTTTGCTTCCTTTACTTTCTGAGAGAAGGCCACTACAACGATGCCC TGGAAGCAGAGATCCATGTTGTGGCAGCTGGTATGATAATGCGTGGTAGTGACGGGGCGA TAGAGGCTGTTTGGATTGAGCCAGGGTCCGCCTCGCCGACCGCGGGCGCGCCAATTTATT GCCGGCCGATTCCGCCGCCCGTGTCTCGCTAACAAATTGGTGCTGGATTGTAGACAGGTA AGGCCAGGGCGCATCAATTACTTCCCCCATTCCTAAATATAAGTTTTTTAAAGGTTTCAT TAGGGAATACATACGGATGTATATAAACATGTTAGTGTAGATTTCCTCATTTTGTTTTGT ATGTAGTCTTCTAGTGAAATCTTTAAAAAAAAACTTTATATTTAAAAACGAA
Protein Sequence (394 aa)
>BART1_0-u53404.006 394 150831_barley_pseudomolecules GWRWRRRRRRRRRRFPQRRSSVRTAASAQPTCSRPPRSVRARIEVAVLNFLALLSSPSSP SISVLPLISRKSTNCSLRSGLLSDVSSVYLSYAFCKRSLMRENDAKAFVRVWKVMEMCYK ILGEGKLVTQRELFYKLLSDSPKYFSCQRHVNQTIQDVVSLLRCTRQSLGIMASSRGALI GRLVLHEPEEEHIDCSILGPSGHAITGDLNQLSRLNLSSDARYLILVEKDAIFQRLAEDR LYNQLPCILITAKGYPDIATRFILHRLSQTFPNMPIFALVDWNPAGLSILCTYKYGSISM GLESYRYACNVKWLGLRGDDLQLIPQSSFQELKPRDLQVAKSLLSSKFLQDTHRAELTRM VETGTRAEIEALYCHGFDFLGKFIARKIVQGDYI