- Transcript BART1_0-u12547.020
- Transcript IDBART1_0-u12547.020
- Gene IDBART1_0-u12547
Barley RTD
Exon Structure of BART1_0-u12547.020
| Chromosome | Exon | Start | Stop | Direction |
|---|---|---|---|---|
| chr2H | 1 | 554963517 | 554962827 | - |
| chr2H | 2 | 554964049 | 554963996 | - |
| chr2H | 3 | 554964276 | 554964158 | - |
| chr2H | 4 | 554964452 | 554964390 | - |
| chr2H | 5 | 554965007 | 554964530 | - |
| chr2H | 6 | 554965179 | 554965082 | - |
| chr2H | 7 | 554966070 | 554965968 | - |
| chr2H | 8 | 554967079 | 554966975 | - |
| chr2H | 9 | 554967248 | 554967169 | - |
| chr2H | 10 | 554967462 | 554967364 | - |
| chr2H | 11 | 554967608 | 554967557 | - |
| chr2H | 12 | 554968422 | 554968316 | - |
| chr2H | 13 | 554970131 | 554969638 | - |
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 | 0.743592 |
| morex | ETI | 1.4383 | 0 | 1.85592 |
| morex | LEA | 0 | 0 | 0 |
| morex | EPI | 0 | 1.71065 | 1.37481 |
| morex | ROO | 0.627278 | 0 | 0.388233 |
| morex | ROO2 | 2.48889 | 1.22607 | 0.960164 |
| morex | NOD | 2.05472 | 2.43558 | 1.21069 |
| morex | RAC | 0 | 1.91162 | 1.94284 |
| morex | INF1 | 0 | 0 | 0 |
| morex | INF2 | 0 | 0 | 0.0909006 |
| morex | CAR5 | 2.2575 | 1.87008 | 4.07906 |
| morex | CAR15 | 2.94349 | 3.51427 | 2.55367 |
| morex | LEM | 1.84808 | 0.0000013416 | 0.460031 |
| morex | LOD | 0 | 2.01304 | 0.784092 |
| morex | PAL | 0.000000312411 | 1.91738 | 0.694042 |
| morex | SEN | 0.650996 | 0.101669 | 2.20866 |
Homology to Model Species (BLASTX to E-value < 1e-30)
| Database | Hit | Frame | E-value | Score | % Identity | Description |
|---|---|---|---|---|---|---|
| Rice PP7 | LOC_Os04g35920.2 | +2 | 0.0 | 495 | 320/415 (77%) | protein|nonsense-mediated decay UPF3, putative, expressed |
| TAIR PP10 | AT1G33980 @ ARAPORT AT1G33980.1 @ TAIR |
+2 | 1e-62 | 137 | 143/443 (32%) | Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482 |
| BRACH PP3 | Bradi5g10820.2.p | +2 | 0.0 | 536 | 335/415 (81%) | pacid=32810360 transcript=Bradi5g10820.2 locus=Bradi5g10820 ID=Bradi5g10820.2.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 (2543 bp)
>BART1_0-u12547.020 2543 150831_barley_pseudomolecules TTCGTTTCGTCCTCGTCGTCGTCCTCCCTCTTCCACCCCCCTTCCCAATCTCCGACAGTT TCCAATTTCTCATCTCCCAACCCCAAACCCCAACCCCAACCAGAGACCGAAAAGAGTCGC ACGCGACTTCGCGAGAGGGGGGAAGCAGCAGACGAGAGCGAGAGACCTCCTCCTTCCCCA ACCCCGCCCCAAACCCTAACCCTTCATCAGATCTCGCGCCCGTCTGCCCTCCCGCCCCGT CCCGCCTCGATGTGACCCGGCCCCTAGGGTTTGTGCCGGCGCGGTGTGGTGGTGGGTCCC GGTTCGTGGGCGGATTTCGGACCCGAGGAGTTGGAGCTGGAGGCGCGCGCGCACATGAAG GACCCGGCGCACCGCACGAAGGTGGTGCTCAGGCGGCTGCCGCCGGCGATTGCGCAGCAG GCCGTCGTGGACCAGGTTGACGCGCGCTTCGCTGGGCGCTATGACTGGGCCCGTTTCCGC CCCGGTAATGCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGC CCAGAAGATGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAA GGTTCCGAAGTCAAATATCAAGAAAGATGCTCGTCAAGGAACTATAACAAAAGATCCAGA ATACTTGGAGTTTCTTGAGCTTATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAAT TCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTAC ACCTCTTATGGTTTATGTTCGTCAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGT AAGTAGCAGACTAAGCAGAAAAGTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAA AAGGTCTTCTGAAAGGCGCAGGGCCTCCACTTCAACGCAGTATGTTGTGCGAGACAATGC TAAGGAAAAGCCGACTTACATCTTAGCACCAAAGAGAGATGATCATACACAGAGAGAGAA AATCATTGCTGGAACTTCAGATGCTACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTAT CGACGGTAAAAGGGACAAAATTGTCCTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATAT ATCTGATAGCTCAACCCCGCAGCAGTCTGTGCCCCCGTCGAGAAATACACCTCCATCAAC TTCTAGACAAGACCAGCGAAATGAGGCCAGTGGCAGAATTATCAAGACTATACTTTCAAA CAAGGAAGGACGCCATGCAATAGCATCTCAACATGAGCAAGAAGGTCACATAATTAGTGC CGAGAAGGATAAGAGGCCACCACGGGCTCCAAACTCGCGTTCCACTGCAAAAGATCAGAT TGTTGAAAATGCTGAGAAAAACCATTATGATGACAAGCATAATCATGTGCATGGTTCTGG ACCCATTGGTGAGAAGATTGAAAGACATGCCAGAAATAGAGATAGGCCTGACCGAGGTGT TTGGGCCCCTCGTCGCTATGACAAGTCTGCATCAGGAGGCGGTGCGCAAGCCTCATTGTC TGAGTTCCCGCTAATGCAGTCACACTCTATGGACAATGTATCTCAGCAAGTAGATGGCCA TGGAGAGCGAAAAATAGACACAAGGGGTCCTGGTGGCCGCGGTGGCCTTGTGGAGAATGG AAACAGGCACCCCAACCGCCGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAATCCCTCC TATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCATGAGAG ACAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGTGAGTTTGTCCACCAATGATACTTTC ATCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTCTGATTG TGAATGAAATGACTGTTGGTGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGTCAACGG AAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGATTTGATTCACAGAATCACAGCAATA GTGAAGTAACATAACCCACCAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTTGATTTT GGACCCAAGGGTGCTATATCTGGAGGGACGGATGGAAATTAGGCTGGCATCAATACCTCG AGACAGTGGTCACATATTTCCAAGACCCCTGGAGGCTATACACAAACCCGACGATTCATC AGTGATGGATGTACATATCTCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGTTTACAG GTTAGAGGTGCCATGTATCTACAAAGAGATAAGAGTTACCAGACTACCCAGTTTGCTAAA TAAAGGTGAATTTTTAGTTAGTTGATTATGAGAACCCCTGTATCCCGGCGGCTGCAGTTG CAGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAAGTGACAGCACTATCATGTTTTATGC TCCAGGTTGAATGGAATGTGAGGCTATTTTGCTTGCTGATGTTGTGTTTTCTACTGTGAC GTCACTCACCATATAAGTTTTTT
Protein Sequence (414 aa)
>BART1_0-u12547.020 414 150831_barley_pseudomolecules MKKVPKSNIKKDARQGTITKDPEYLEFLELISKPTEHLPSAEIQLERKEAERAAAGKEPP VITPLMVYVRQQRAAKSMAQRSVSSRLSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVR DNAKEKPTYILAPKRDDHTQREKIIAGTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVD SNISDSSTPQQSVPPSRNTPPSTSRQDQRNEASGRIIKTILSNKEGRHAIASQHEQEGHI ISAEKDKRPPRAPNSRSTAKDQIVENAEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPD RGVWAPRRYDKSASGGGAQASLSEFPLMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLV ENGNRHPNRRGPPRGPKEMEIPPIASDGKPSKRGPASYVAHERQVWVQKSSSGS