Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u12547.007

ChromosomeExonStartStopDirection
chr2H1554963517554962472-
chr2H2554964049554963996-
chr2H3554964276554964158-
chr2H4554964452554964390-
chr2H5554965007554964530-
chr2H6554965179554965082-
chr2H7554966070554965968-
chr2H8554967079554966975-
chr2H9554967248554967169-
chr2H10554967462554967364-
chr2H11554967652554967557-
chr2H12554968422554968316-
chr2H13554970295554969638-


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
morexETI000
morexLEA000
morexEPI000
morexROO000
morexROO2000
morexNOD000.464093
morexRAC000
morexINF10.000000001436330.00000002028050.000647991
morexINF200.6792920.0000413943
morexCAR500.01257890.000796408
morexCAR150.00002772110.000000001129170.0000607486
morexLEM000
morexLOD000
morexPAL000
morexSEN000



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 0.0 726 431/510 (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 (3106 bp)

>BART1_0-u12547.007 3106 150831_barley_pseudomolecules
CTCCATATATATCTATAGGGAACTTGTTCAAAAATGCCATAGCCAGCTTTTTTTTATGCA
TCAACCTACTTTACATTATTATATCAGGACTGAGGATGGGTATTTTTCTCGTATCTTTGC
TTGCGTTGCGCCTTCCCTTTTTTTTCCCCTTCCCGTGTCGCCTTTTCGTTTCGTCCTCGT
CGTCGTCCTCCCTCTTCCACCCCCCTTCCCAATCTCCGACAGTTTCCAATTTCTCATCTC
CCAACCCCAAACCCCAACCCCAACCAGAGACCGAAAAGAGTCGCACGCGACTTCGCGAGA
GGGGGGAAGCAGCAGACGAGAGCGAGAGACCTCCTCCTTCCCCAACCCCGCCCCAAACCC
TAACCCTTCATCAGATCTCGCGCCCGTCTGCCCTCCCGCCCCGTCCCGCCTCGATGTGAC
CCGGCCCCTAGGGTTTGTGCCGGCGCGGTGTGGTGGTGGGTCCCGGTTCGTGGGCGGATT
TCGGACCCGAGGAGTTGGAGCTGGAGGCGCGCGCGCACATGAAGGACCCGGCGCACCGCA
CGAAGGTGGTGCTCAGGCGGCTGCCGCCGGCGATTGCGCAGCAGGCCGTCGTGGACCAGG
TTGACGCGCGCTTCGCTGGGCGCTATGACTGGGCCCGTTTCCGCCCCGGTAATGCCAGCC
AAAAGAATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGCCCAGAAGATGTTGTTG
AGTTTGCTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAAGGTGCTCAATTTAAAG
CTCTTGTGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAGAAAGATGCTC
GTCAAGGAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTTATATCAAAGC
CCACTGAGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAG
CTGCTGGAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGTCAGCAAAGGG
CGGCTAAGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAAGTTGCAGGTG
TGGTAACCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGGGCCTCCACTT
CAACGCAGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTAGCACCAA
AGAGAGATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCTACAAGCG
GAGGGCCATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTCCTCCTTA
AAGGAAGAGCGAGGGTTGATTCCAATATATCTGATAGCTCAACCCCGCAGCAGTCTGTGC
CCCCGTCGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAGTG
GCAGAATTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCTCAAC
ATGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCCAA
ACTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTATGATG
ACAAGCATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACATGCCA
GAAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGCAT
CAGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTATGG
ACAATGTATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCCTG
GTGGCCGCGGTGGCCTTGTGGAGAATGGAAACAGGCACCCCAACCGCCGTGGTCCGCCAC
GTGGGCCGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAGGG
GCCCTGCTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGGAT
CGTGAGTTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAAGT
CTCTGGATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGGTGAGATGGTTCTG
TGAAGTGCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTCTT
TGATTTGATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCACCAGTAGGTAGCTC
TCCATCACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATATCTGGAGGGACGGA
TGGAAATTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATTTCCAAGACCCCTGG
AGGCTATACACAAACCCGACGATTCATCAGTGATGGATGTACATATCTCTAGAGAAAGAA
GAGGTCTGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATCTACAAAGAGATAA
GAGTTACCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATGAG
AACCCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGTGC
AAAGTGACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGTGAGGCTATTTTGC
TTGCTGATGTTGTGTTTTCTACTGTGACGTCACTCACCATATAAGTTTTTTTGGGGTTAC
GTTAAGAATTATATGCATGGTTATGGTGTACGCCATCAAAGGTGGTTGCTGTTTTTATTA
TCAGCAACAGGTATGTTTGACTTGCGCTGTTGATGTTCTGTCAGACAGGCAAGCTGTTGT
TGTTAGTAATTCTTGTAAACACTTGCAGATCTGCCTATGGGTCGTGCGCGCACTGATCGG
AGGAGGCAAAGTTCTCTTATTCTTGTAAGGGGAATTAGATCGTTCAATTAAACTACAAAG
TCGCTGGTTAACTACTTACAATGCAGCTGGGATCAATTTCTTCCCAAGAATAGTCATACT
TAGCGAGTTTGTCAGCAACACCATAACCATGCCTATTGAAAGGGAA



Protein Sequence (508 aa)

>BART1_0-u12547.007 508 150831_barley_pseudomolecules
MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF
KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE
FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR
LSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVRDNAKEKPTYILAPKRDDHTQREKIIA
GTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNISDSSTPQQSVPPSRNTPPSTSRQ
DQRNEASGRIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVEN
AEKNHYDDKHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFP
LMQSHSMDNVSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRGPKEMEIPPIAS
DGKPSKRGPASYVAHERQVWVQKSSSGS