Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u12547.011

ChromosomeExonStartStopDirection
chr2H1554963517554962621-
chr2H2554964049554963996-
chr2H3554964276554964158-
chr2H4554964452554964390-
chr2H5554964983554964530-
chr2H6554965179554965082-
chr2H7554966070554965968-
chr2H8554967079554966975-
chr2H9554967248554967169-
chr2H10554967462554967364-
chr2H11554967652554967557-
chr2H12554968422554968316-
chr2H13554970201554969638-


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
morexEMB1.50970.004792550.0584239
morexETI0.00000007137462.309150.000000000149298
morexLEA001.36407
morexEPI0.6098920.0119950.00466633
morexROO0.9709450.01762480
morexROO21.460710.0002456240
morexNOD2.045280.00000001424233.84752
morexRAC0.00000046317400
morexINF11.566265.605313.3454
morexINF20.000000004741874.137663.63364
morexCAR500.00000004183710.431248
morexCAR150.4941150.8291970
morexLEM000
morexLOD000.00000000641697
morexPAL0.0000000025005900.764799
morexSEN1.3317900.000000452458



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os04g35920.2 +2 0.0 683 411/514 (80%) protein|nonsense-mediated decay UPF3, putative, expressed
TAIR PP10 AT1G33980 @ ARAPORT
AT1G33980.1 @ TAIR		 +2 2e-84 280 205/530 (39%) Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482
BRACH PP3 Bradi5g10820.2.p +2 0.0 710 426/510 (84%) 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 (2839 bp)

>BART1_0-u12547.011 2839 150831_barley_pseudomolecules
GATGGGTATTTTTCTCGTATCTTTGCTTGCGTTGCGCCTTCCCTTTTTTTTCCCCTTCCC
GTGTCGCCTTTTCGTTTCGTCCTCGTCGTCGTCCTCCCTCTTCCACCCCCCTTCCCAATC
TCCGACAGTTTCCAATTTCTCATCTCCCAACCCCAAACCCCAACCCCAACCAGAGACCGA
AAAGAGTCGCACGCGACTTCGCGAGAGGGGGGAAGCAGCAGACGAGAGCGAGAGACCTCC
TCCTTCCCCAACCCCGCCCCAAACCCTAACCCTTCATCAGATCTCGCGCCCGTCTGCCCT
CCCGCCCCGTCCCGCCTCGATGTGACCCGGCCCCTAGGGTTTGTGCCGGCGCGGTGTGGT
GGTGGGTCCCGGTTCGTGGGCGGATTTCGGACCCGAGGAGTTGGAGCTGGAGGCGCGCGC
GCACATGAAGGACCCGGCGCACCGCACGAAGGTGGTGCTCAGGCGGCTGCCGCCGGCGAT
TGCGCAGCAGGCCGTCGTGGACCAGGTTGACGCGCGCTTCGCTGGGCGCTATGACTGGGC
CCGTTTCCGCCCCGGTAATGCCAGCCAAAAGAATCATAGATATTCTCGTCTCTACCTTAA
CTTCAAGAGCCCAGAAGATGTTGTTGAGTTTGCTGAGTTCTTCAATGGGCATGTATTTGT
GAATGAAAAAGGTGCTCAATTTAAAGCTCTTGTGGAATATGCACCATCACAACAGGTTCC
GAAGTCAAATATCAAGAAAGATGCTCGTCAAGGAACTATAACAAAAGATCCAGAATACTT
GGAGTTTCTTGAGCTTATATCAAAGCCCACTGAGCATTTGCCAAGTGCTGAAATTCAGCT
TGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTGGAAAGGAGCCACCTGTTATTACACCTCT
TATGGTTTATGTTCGTCAGCAAAGGGCGGCTAAGAGTATGGCTCAGAGGTCTGTAAGTAG
CAGACTAAGCAGAAAAGTTGCAGGTGTGGTAACCAGTAGTTCTAGTCCATCTAAAAGGTC
TTCTGAAAGGCGCAGGGCCTCCACTTCAACGCAGTATGTTGTGCGAGACAATGCTAAGGA
AAAGCCGACTTACATCTTAGCACCAAAGAGAGATGATCATACACAGAGAGAGAAAATCAT
TGCTGGAACTTCAGATGCTACAAGCGGAGGGCCATCTGGGTCTGCTCAGGTTATCGACGG
TAAAAGGGACAAAATTGTCCTCCTTAAAGGAAGAGCGAGGGTTGATTCCAATCAGTCTGT
GCCCCCGTCGAGAAATACACCTCCATCAACTTCTAGACAAGACCAGCGAAATGAGGCCAG
TGGCAGAATTATCAAGACTATACTTTCAAACAAGGAAGGACGCCATGCAATAGCATCTCA
ACATGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGGATAAGAGGCCACCACGGGCTCC
AAACTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAAATGCTGAGAAAAACCATTATGA
TGACAAGCATAATCATGTGCATGGTTCTGGACCCATTGGTGAGAAGATTGAAAGACATGC
CAGAAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCCCTCGTCGCTATGACAAGTCTGC
ATCAGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCCCGCTAATGCAGTCACACTCTAT
GGACAATGTATCTCAGCAAGTAGATGGCCATGGAGAGCGAAAAATAGACACAAGGGGTCC
TGGTGGCCGCGGTGGCCTTGTGGAGAATGGAAACAGGCACCCCAACCGCCGTGGTCCGCC
ACGTGGGCCGAAGGAGATGGAAATCCCTCCTATTGCATCTGATGGAAAGCCTTCGAAGAG
GGGCCCTGCTAGCTATGTGGCTCATGAGAGACAAGTATGGGTTCAGAAGTCAAGTTCAGG
ATCGTGAGTTTGTCCACCAATGATACTTTCATCAAAATAGATGTTGCAAGTTGTGGAGAA
GTCTCTGGATTTTGCGGCTCATTCTGATTGTGAATGAAATGACTGTTGGTGAGATGGTTC
TGTGAAGTGCAATTCCAGATTTGTCAACGGAAGTCTCAGCTATAGCTGAAAAAGCAGCTC
TTTGATTTGATTCACAGAATCACAGCAATAGTGAAGTAACATAACCCACCAGTAGGTAGC
TCTCCATCACTTTGGGTGAGATTTGATTTTGGACCCAAGGGTGCTATATCTGGAGGGACG
GATGGAAATTAGGCTGGCATCAATACCTCGAGACAGTGGTCACATATTTCCAAGACCCCT
GGAGGCTATACACAAACCCGACGATTCATCAGTGATGGATGTACATATCTCTAGAGAAAG
AAGAGGTCTGGCTCTGATTGCTGTTTACAGGTTAGAGGTGCCATGTATCTACAAAGAGAT
AAGAGTTACCAGACTACCCAGTTTGCTAAATAAAGGTGAATTTTTAGTTAGTTGATTATG
AGAACCCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGTAAGACCGAAGTTACCGTGGAGT
GCAAAGTGACAGCACTATCATGTTTTATGCTCCAGGTTGAATGGAATGTGAGGCTATTTT
GCTTGCTGATGTTGTGTTTTCTACTGTGACGTCACTCACCATATAAGTTTTTTTGGGGTT
ACGTTAAGAATTATATGCATGGTTATGGTGTACGCCATCAAAGGTGGTTGCTGTTTTTAT
TATCAGCAACAGGTATGTTTGACTTGCGCTGTTGATGTTCTGTCAGACAGGCAAGCTGTT
GTTGTTAGTAATTCTTGTAAACACTTGCAGATCTGCCTATGGGTCGTGCGCGCACTGATC
GGAGGAGGCAAAGTTCTCT



Protein Sequence (500 aa)

>BART1_0-u12547.011 500 150831_barley_pseudomolecules
MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF
KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE
FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR
LSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVRDNAKEKPTYILAPKRDDHTQREKIIA
GTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNQSVPPSRNTPPSTSRQDQRNEASG
RIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVENAEKNHYDD
KHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFPLMQSHSMD
NVSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRGPKEMEIPPIASDGKPSKRG
PASYVAHERQVWVQKSSSGS