Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u12547.005

ChromosomeExonStartStopDirection
chr2H1554962669554962365-
chr2H2554963517554962748-
chr2H3554964049554963996-
chr2H4554964276554964158-
chr2H5554964452554964390-
chr2H6554965007554964530-
chr2H7554965179554965082-
chr2H8554966070554965968-
chr2H9554967079554966975-
chr2H10554967248554967169-
chr2H11554967462554967364-
chr2H12554967652554967557-
chr2H13554968422554968316-
chr2H14554970229554969638-


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


SampleTreatmentRep 1Rep 2Rep 3
morexEMB000
morexETI0.3780540.3948710
morexLEA000
morexEPI000
morexROO000
morexROO2000
morexNOD000.465463
morexRAC000
morexINF10.00000000078103700.0000000254873
morexINF20.9437320.04255830.00000124721
morexCAR500.838030.0000053341
morexCAR151.993820.00009285250.595494
morexLEM00.4008110.226463
morexLOD000
morexPAL000.296284
morexSEN000.26656



Homology to Model Species (BLASTX to E-value < 1e-30)

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os04g35920.2 +3 0.0 696 414/514 (81%) protein|nonsense-mediated decay UPF3, putative, expressed
TAIR PP10 AT1G33980 @ ARAPORT
AT1G33980.1 @ TAIR		 +3 3e-85 283 206/538 (38%) Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482
BRACH PP3 Bradi5g10820.2.p +3 0.0 727 431/510 (85%) 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 (3069 bp)

>BART1_0-u12547.005 3069 150831_barley_pseudomolecules
TACTTTACATTATTATATCAGGACTGAGGATGGGTATTTTTCTCGTATCTTTGCTTGCGT
TGCGCCTTCCCTTTTTTTTCCCCTTCCCGTGTCGCCTTTTCGTTTCGTCCTCGTCGTCGT
CCTCCCTCTTCCACCCCCCTTCCCAATCTCCGACAGTTTCCAATTTCTCATCTCCCAACC
CCAAACCCCAACCCCAACCAGAGACCGAAAAGAGTCGCACGCGACTTCGCGAGAGGGGGG
AAGCAGCAGACGAGAGCGAGAGACCTCCTCCTTCCCCAACCCCGCCCCAAACCCTAACCC
TTCATCAGATCTCGCGCCCGTCTGCCCTCCCGCCCCGTCCCGCCTCGATGTGACCCGGCC
CCTAGGGTTTGTGCCGGCGCGGTGTGGTGGTGGGTCCCGGTTCGTGGGCGGATTTCGGAC
CCGAGGAGTTGGAGCTGGAGGCGCGCGCGCACATGAAGGACCCGGCGCACCGCACGAAGG
TGGTGCTCAGGCGGCTGCCGCCGGCGATTGCGCAGCAGGCCGTCGTGGACCAGGTTGACG
CGCGCTTCGCTGGGCGCTATGACTGGGCCCGTTTCCGCCCCGGTAATGCCAGCCAAAAGA
ATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGCCCAGAAGATGTTGTTGAGTTTG
CTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAAGGTGCTCAATTTAAAGCTCTTG
TGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAGAAAGATGCTCGTCAAG
GAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTTATATCAAAGCCCACTG
AGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTG
GAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGTCAGCAAAGGGCGGCTA
AGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAAGTTGCAGGTGTGGTAA
CCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGGGCCTCCACTTCAACGC
AGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTAGCACCAAAGAGAG
ATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCTACAAGCGGAGGGC
CATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTCCTCCTTAAAGGAA
GAGCGAGGGTTGATTCCAATATATCTGATAGCTCAACCCCGCAGCAGTCTGTGCCCCCGT
CGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAGTGGCAGAA
TTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCTCAACATGAGC
AAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCCAAACTCGC
GTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTATGATGACAAGC
ATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACATGCCAGAAATA
GAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGCATCAGGAG
GCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTATGGACAATG
TATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCCTGGTGGCC
GCGGTGGCCTTGTGGAGAATGGAAACAGGCACCCCAACCGCCGTGGTCCGCCACGTGGGC
CGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCCCTG
CTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGTGAG
TTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTCTGG
ATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTGTGAAGT
GCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGATTT
GATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCACCAGTAGGTAGCTCTCCATC
ACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGATGGAAA
TTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATTTCCAAGACCCCTGGAGGCTA
TACACAAACCCGACGATTCATCAGTGATGGATGTACATATCTCTAGAGAAAGAAGAGGTC
TGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAAGAGTTA
CCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAGAACCCC
TGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAAGTG
ACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGTGAGGCTATTTTGCTTGCTG
ATGTTGTGTTTTCTACTGTGACGTCACTCACCATATAAGTTTTTTTGGGGTTACGTTAAG
AATTATATGCATGGTTATGGTGTACGCCATCAAAGGTGGTTGCTGTTTTTATTATCAGCA
ACAGATCTGCCTATGGGTCGTGCGCGCACTGATCGGAGGAGGCAAAGTTCTCTTATTCTT
GTAAGGGGAATTAGATCGTTCAATTAAACTACAAAGTCGCTGGTTAACTACTTACAATGC
AGCTGGGATCAATTTCTTCCCAAGAATAGTCATACTTAGCGAGTTTGTCAGCAACACCAT
AACCATGCCTATTGAAAGGGAACGAAGAAGAAACAGGAAAAGGGAGTTCGGACTGTTACT
TCGCCTAATATTGACCGTCCTGGTCCATCAAAAACCACTTTTCCCTTCCGCTCACCTGGT
CGAGGATGG



Protein Sequence (508 aa)

>BART1_0-u12547.005 508 150831_barley_pseudomolecules
MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF
KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE
FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR
LSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVRDNAKEKPTYILAPKRDDHTQREKIIA
GTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNISDSSTPQQSVPPSRNTPPSTSRQ
DQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVEN
AEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFP
LMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRGPKEMEIPPIAS
DGKPSKRGPASYVAHERQVWVQKSSSGS