Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u12547.008

ChromosomeExonStartStopDirection
chr2H1554962669554962472-
chr2H2554963517554962748-
chr2H3554964049554963996-
chr2H4554964276554964158-
chr2H5554964452554964390-
chr2H6554964983554964530-
chr2H7554965179554965082-
chr2H8554966067554965968-
chr2H9554967079554966975-
chr2H10554967248554967169-
chr2H11554967462554967364-
chr2H12554967652554967557-
chr2H13554968422554968316-
chr2H14554970173554969638-


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
morexETI0.000000079310600
morexLEA000
morexEPI000
morexROO1.2861300
morexROO2000
morexNOD0.000000012914900
morexRAC000
morexINF1000
morexINF2000
morexCAR5000
morexCAR150.00022853700
morexLEM000
morexLOD000
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os04g35920.2 +1 0.0 677 402/514 (78%) protein|nonsense-mediated decay UPF3, putative, expressed
TAIR PP10 AT1G33980 @ ARAPORT
AT1G33980.1 @ TAIR		 +1 4e-85 282 204/529 (39%) Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482
BRACH PP3 Bradi5g10820.2.p +1 0.0 713 419/509 (82%) 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 (2879 bp)

>BART1_0-u12547.008 2879 150831_barley_pseudomolecules
GCGTTGCGCCTTCCCTTTTTTTTCCCCTTCCCGTGTCGCCTTTTCGTTTCGTCCTCGTCG
TCGTCCTCCCTCTTCCACCCCCCTTCCCAATCTCCGACAGTTTCCAATTTCTCATCTCCC
AACCCCAAACCCCAACCCCAACCAGAGACCGAAAAGAGTCGCACGCGACTTCGCGAGAGG
GGGGAAGCAGCAGACGAGAGCGAGAGACCTCCTCCTTCCCCAACCCCGCCCCAAACCCTA
ACCCTTCATCAGATCTCGCGCCCGTCTGCCCTCCCGCCCCGTCCCGCCTCGATGTGACCC
GGCCCCTAGGGTTTGTGCCGGCGCGGTGTGGTGGTGGGTCCCGGTTCGTGGGCGGATTTC
GGACCCGAGGAGTTGGAGCTGGAGGCGCGCGCGCACATGAAGGACCCGGCGCACCGCACG
AAGGTGGTGCTCAGGCGGCTGCCGCCGGCGATTGCGCAGCAGGCCGTCGTGGACCAGGTT
GACGCGCGCTTCGCTGGGCGCTATGACTGGGCCCGTTTCCGCCCCGGTAATGCCAGCCAA
AAGAATCATAGATATTCTCGTCTCTACCTTAACTTCAAGAGCCCAGAAGATGTTGTTGAG
TTTGCTGAGTTCTTCAATGGGCATGTATTTGTGAATGAAAAAGGTGCTCAATTTAAAGCT
CTTGTGGAATATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAGAAAGATGCTCGT
CAAGGAACTATAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTTATATCAAAGCCC
ACTGAGCATTTGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAGCT
GCTGGAAAGGAGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGTCAGCAAAGGGCG
GCTAAGAGTATGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAAGTTGCAGGTGTG
GTAACCAGTAGTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGGGCCTCCACTTCA
ACGTATGTTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTAGCACCAAAGAGA
GATGATCATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCTACAAGCGGAGGG
CCATCTGGGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTCCTCCTTAAAGGA
AGAGCGAGGGTTGATTCCAATCAGTCTGTGCCCCCGTCGAGAAATACACCTCCATCAACT
TCTAGACAAGACCAGCGAAATGAGGCCAGTGGCAGAATTATCAAGACTATACTTTCAAAC
AAGGAAGGACGCCATGCAATAGCATCTCAACATGAGCAAGAAGGTCACATAATTAGTGCC
GAGAAGGATAAGAGGCCACCACGGGCTCCAAACTCGCGTTCCACTGCAAAAGATCAGATT
GTTGAAAATGCTGAGAAAAACCATTATGATGACAAGCATAATCATGTGCATGGTTCTGGA
CCCATTGGTGAGAAGATTGAAAGACATGCCAGAAATAGAGATAGGCCTGACCGAGGTGTT
TGGGCCCCTCGTCGCTATGACAAGTCTGCATCAGGAGGCGGTGCGCAAGCCTCATTGTCT
GAGTTCCCGCTAATGCAGTCACACTCTATGGACAATGTATCTCAGCAAGTAGATGGCCAT
GGAGAGCGAAAAATAGACACAAGGGGTCCTGGTGGCCGCGGTGGCCTTGTGGAGAATGGA
AACAGGCACCCCAACCGCCGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAATCCCTCCT
ATTGCATCTGATGGAAAGCCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCATGAGAGA
CAAGTATGGGTTCAGAAGTCAAGTTCAGGATCGTGAGTTTGTCCACCAATGATACTTTCA
TCAAAATAGATGTTGCAAGTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTCTGATTGT
GAATGAAATGACTGTTGGTGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGTCAACGGA
AGTCTCAGCTATAGCTGAAAAAGCAGCTCTTTGATTTGATTCACAGAATCACAGCAATAG
TGAAGTAACATAACCCACCAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTTGATTTTG
GACCCAAGGGTGCTATATCTGGAGGGACGGATGGAAATTAGGCTGGCATCAATACCTCGA
GACAGTGGTCACATATTTCCAAGACCCCTGGAGGCTATACACAAACCCGACGATTCATCA
GTGATGGATGTACATATCTCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGTTTACAGG
TTAGAGGTGCCATGTATCTACAAAGAGATAAGAGTTACCAGACTACCCAGTTTGCTAAAT
AAAGGTGAATTTTTAGTTAGTTGATTATGAGAACCCCTGTATCCCGGCGGCTGCAGTTGC
AGTCAGTAAGACCGAAGTTACCGTGGAGTGCAAAGTGACAGCACTATCATGTTTTATGCT
CCAGGTTGAATGGAATGTGAGGCTATTTTGCTTGCTGATGTTGTGTTTTCTACTGTGACG
TCACTCACCATATAAGTTTTTTTGGGGTTACGTTAAGAATTATATGCATGGTTATGGTGT
ACGCCATCAAAGGTGGTTGCTGTTTTTATTATCAGCAACAGATCTGCCTATGGGTCGTGC
GCGCACTGATCGGAGGAGGCAAAGTTCTCTTATTCTTGTAAGGGGAATTAGATCGTTCAA
TTAAACTACAAAGTCGCTGGTTAACTACTTACAATGCAGCTGGGATCAATTTCTTCCCAA
GAATAGTCATACTTAGCGAGTTTGTCAGCAACACCATAACCATGCCTATTGAAAGGGAA



Protein Sequence (499 aa)

>BART1_0-u12547.008 499 150831_barley_pseudomolecules
MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF
KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE
FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR
LSRKVAGVVTSSSSPSKRSSERRRASTSTYVVRDNAKEKPTYILAPKRDDHTQREKIIAG
TSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNQSVPPSRNTPPSTSRQDQRNEASGR
IIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVENAEKNHYDDK
HNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFPLMQSHSMDN
VSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRGPKEMEIPPIASDGKPSKRGP
ASYVAHERQVWVQKSSSGS