- Transcript BART1_0-u34851.004
- Transcript IDBART1_0-u34851.004
- Gene IDBART1_0-u34851
Barley RTD
Exon Structure of BART1_0-u34851.004
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr5H | 1 | 280032568 | 280031539 | + |
| chr5H | 2 | 280032882 | 280032720 | + |
| chr5H | 3 | 280033483 | 280033289 | + |
| chr5H | 4 | 280034038 | 280033780 | + |
| chr5H | 5 | 280034588 | 280034140 | + |
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 | 2.10601 | 6.14107 | 18.1853 |
| morex | LEA | 0.0000257528 | 0 | 2.01083 |
| morex | EPI | 47.4136 | 17.5054 | 46.7028 |
| morex | ROO | 0 | 0 | 0 |
| morex | ROO2 | 0.10544 | 0.0543061 | 0 |
| morex | NOD | 0 | 0 | 0 |
| morex | RAC | 8.06324 | 4.55397 | 4.59403 |
| morex | INF1 | 0 | 0 | 0 |
| morex | INF2 | 0 | 0 | 0 |
| morex | CAR5 | 0 | 1.28153 | 0.519417 |
| morex | CAR15 | 0.855899 | 1.60318 | 1.70033 |
| morex | LEM | 0.0815348 | 0.0510594 | 7.91878 |
| morex | LOD | 0.0159495 | 0.670435 | 0 |
| morex | PAL | 4.83262 | 5.01022 | 4.30975 |
| morex | SEN | 12.0096 | 7.43492 | 3.41748 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os12g31000.1 | +3 | 6e-105 | 330 | 208/369 (56%) | protein|pumilio-family RNA binding repeat domain containing protein, expressed |
| TAIR PP10 | AT1G78160 @ ARAPORT AT1G78160.1 @ TAIR |
+1 | 8e-97 | 194 | 93/175 (53%) | Symbols: APUM7, PUM7 | pumilio 7 | chr1:29407900-29410184 FORWARD LENGTH=650 |
| BRACH PP3 | Bradi4g07100.1.p | +3 | 0.0 | 439 | 240/330 (73%) | pacid=32788499 transcript=Bradi4g07100.1 locus=Bradi4g07100 ID=Bradi4g07100.1.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 (2096 bp)
>BART1_0-u34851.004 2096 150831_barley_pseudomolecules GGTAATAACCTTTCAAAAGAAAAGATTTAAAAGAAGAAGAAAAAAAGCACTCCTCTCACC GGCATCAGTCCTCACTACTTTCGCGCTATCCTTATATAAAAGCACCCCCTCTGCTCTCTC CTCCTCCCACTCCTGCATGCCTCAACGAACCATCTCCAGGAAAACACCTCACCCCAATCC AACCCCAAACCAATCCTCTCCACAAACAAATCTAACAGAATTCCCCCACTGATTTTCTCA TCGAGATTCGATCAAGATAGTAGTTGGAGATGAAGCTGGACAGGGAGATGGAGATGCTCC TCAACGAGATCCCTCTCCTCCTCCACGGCGACGTCCTCGGCTGCAGCGAGCCAGCCGCCG CCGAGACCGACGCCGGCGCCGTCGACTTCGCTTATCTCATCCAAGAACTCGGCGAGATGG GGTTCGTCGAGGACGACGACGACGACGACAGTTTCCTTTACCCAAGGAAGGCCAGCTCAT CTCCGACGAGCAACCTCCATTTCATGGACGCTGAGAATTTCGTGGCGTCGCATCCCTTCT CCATGGACAAAGACCGCGAGAGGGCTCTTTTCGATCCGTTTCCCTTCTCCAGCACCTGCT TCGACGCCGCCGTGGGCGACGACTGGGACCTCCTGTGTCGGCCGGTGAGGTCCCGGCTGT GCAAGACGGCGAGGCCGAAGAAGGGTACCTGCAGCAACGGCTGCCAGGCGACGAGCCCCA AGAAGTGCGCGGCGGCGAAGCCGTCCAAGTACGAGAGCCTTGTCGGGCTGCGCGGGTACA TGTACCACGTGGCCAGGGACCAGCACGGCTGCCGGTTCCTCCAGCAGCGGCTCGACGACG GCAAGCGCGAGGTCGATTTCATCTTCACCGGCGTCGCCCGTCACGCCGTCGACCTCATGG TGAACCCATTCGGTAACTACCTCATGCAGAAGCTGCTAGCCGTCTGCAGCGAGGAGCAGA GGATGGGCATCGTGCTGACCCTCACAAAGGAACCCTTCGTGCTCGTCAGGATCTCTCTCA ATGTACATGGGACAAGGGCGGTTCAGAAGCTGATTGAAAGCTTGAAGGCAAGGGAGGAGA TTCAGCTCGTCGTCGCAGCTCTGCGCCCCGGGTTCCTGGAGCTCATAAAGGATCCTAATG GTAATCATGTCGTGCAGAAGTGCTTGCAATCGTTCGGGGCCGATGATAACAAGACATAAT TAACTCACGATCTACAACTTTCAGCCGATCTTCGATGCTGCTGCTATTTACTGCCTTGAT ATTGGGATGCAATGCCATGGCTGCTGCGTCCTACAGCGGTGTATCGCGCGTTCGACTGGT GAGCACAAGGAGAAGCTGGTTGCCGCGATCGCTCGCAATGGGTTCGAACTTGCACAGGAT GCCTATGGAAACTATGTTGTTCAGTATGTGATAGAACTAAAGGTCGCTGCTGCAAATGCA AGTCTGGCACAACAGTTTGAAGGCAAGTACATCCACCTCTCCATGCAGAAGTTCAGCAGC AACGTTGTCGAGAAATGCCTGAAAGTTTTCAAGGAAGCTGACAAAGCGAACATCATCCTG CAGCTCCTTGCTGCGCCGCAGTTCGAGCGGTTGCTTCTGCACCCTTACGCAAACTATGTA GTCTACGCAGCACTTCAGAATTCCAAGGGCTCTCTACACTCTGCACTGACCAACGCGATC CGGCCTCACGTGGAGCTACTCAGGACCAGCCCATACTGCAAGAGGATCTACTCTCGAGCT TTGCTGAAAAAGTGATGGTCTGATGAGACCATCTCACCATGTGTAACAATAAAGATAGTT TGTCTTGTGCTATTTTTTCGGATTCAAAAGGGATAAAAGTGATCTCACCATGTAGATCTT GTATAGATCAAAATTTATTTGGTCATGTACTTCTATGTGCACCTTTATTTGATGCACTCT TCCGTTGCCATAATCCATCTGGAATGGTAAGTTCCGATCTAACAAATCGTCATATAGATG TTGATGCACGTACACAATATTGGTGATGTTTCTTGTAACTTAATGTTTGCATTTTTTTTT GCCCTGCAATTGCTCAACCGAATGCCAAAACATGAAGGCAAATAACTGATTTGCAG
Protein Sequence (309 aa)
>BART1_0-u34851.004 309 150831_barley_pseudomolecules MKLDREMEMLLNEIPLLLHGDVLGCSEPAAAETDAGAVDFAYLIQELGEMGFVEDDDDDD SFLYPRKASSSPTSNLHFMDAENFVASHPFSMDKDRERALFDPFPFSSTCFDAAVGDDWD LLCRPVRSRLCKTARPKKGTCSNGCQATSPKKCAAAKPSKYESLVGLRGYMYHVARDQHG CRFLQQRLDDGKREVDFIFTGVARHAVDLMVNPFGNYLMQKLLAVCSEEQRMGIVLTLTK EPFVLVRISLNVHGTRAVQKLIESLKAREEIQLVVAALRPGFLELIKDPNGNHVVQKCLQ SFGADDNKT