Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u12547.003

ChromosomeExonStartStopDirection
chr2H1554962669554962301-
chr2H2554963517554962748-
chr2H3554964049554963996-
chr2H4554964276554964158-
chr2H5554964452554964390-
chr2H6554964983554964530-
chr2H7554965179554965082-
chr2H8554966070554965968-
chr2H9554967079554966975-
chr2H10554967248554967169-
chr2H11554967462554967364-
chr2H12554967652554967557-
chr2H13554968422554968316-
chr2H14554970163554969638-


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
morexRAC000
morexINF1000
morexINF2000
morexCAR500.00000000342210
morexCAR15000
morexLEM000
morexLOD000
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os04g35920.2 +3 0.0 682 411/514 (80%) protein|nonsense-mediated decay UPF3, putative, expressed
TAIR PP10 AT1G33980 @ ARAPORT
AT1G33980.1 @ TAIR		 +3 1e-83 279 205/530 (39%) Symbols: ATUPF3, UPF3 | Smg-4/UPF3 family protein | chr1:12351719-12354401 FORWARD LENGTH=482
BRACH PP3 Bradi5g10820.2.p +3 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 (3043 bp)

>BART1_0-u12547.003 3043 150831_barley_pseudomolecules
TTCCCTTTTTTTTCCCCTTCCCGTGTCGCCTTTTCGTTTCGTCCTCGTCGTCGTCCTCCC
TCTTCCACCCCCCTTCCCAATCTCCGACAGTTTCCAATTTCTCATCTCCCAACCCCAAAC
CCCAACCCCAACCAGAGACCGAAAAGAGTCGCACGCGACTTCGCGAGAGGGGGGAAGCAG
CAGACGAGAGCGAGAGACCTCCTCCTTCCCCAACCCCGCCCCAAACCCTAACCCTTCATC
AGATCTCGCGCCCGTCTGCCCTCCCGCCCCGTCCCGCCTCGATGTGACCCGGCCCCTAGG
GTTTGTGCCGGCGCGGTGTGGTGGTGGGTCCCGGTTCGTGGGCGGATTTCGGACCCGAGG
AGTTGGAGCTGGAGGCGCGCGCGCACATGAAGGACCCGGCGCACCGCACGAAGGTGGTGC
TCAGGCGGCTGCCGCCGGCGATTGCGCAGCAGGCCGTCGTGGACCAGGTTGACGCGCGCT
TCGCTGGGCGCTATGACTGGGCCCGTTTCCGCCCCGGTAATGCCAGCCAAAAGAATCATA
GATATTCTCGTCTCTACCTTAACTTCAAGAGCCCAGAAGATGTTGTTGAGTTTGCTGAGT
TCTTCAATGGGCATGTATTTGTGAATGAAAAAGGTGCTCAATTTAAAGCTCTTGTGGAAT
ATGCACCATCACAACAGGTTCCGAAGTCAAATATCAAGAAAGATGCTCGTCAAGGAACTA
TAACAAAAGATCCAGAATACTTGGAGTTTCTTGAGCTTATATCAAAGCCCACTGAGCATT
TGCCAAGTGCTGAAATTCAGCTTGAAAGGAAAGAAGCTGAAAGAGCAGCTGCTGGAAAGG
AGCCACCTGTTATTACACCTCTTATGGTTTATGTTCGTCAGCAAAGGGCGGCTAAGAGTA
TGGCTCAGAGGTCTGTAAGTAGCAGACTAAGCAGAAAAGTTGCAGGTGTGGTAACCAGTA
GTTCTAGTCCATCTAAAAGGTCTTCTGAAAGGCGCAGGGCCTCCACTTCAACGCAGTATG
TTGTGCGAGACAATGCTAAGGAAAAGCCGACTTACATCTTAGCACCAAAGAGAGATGATC
ATACACAGAGAGAGAAAATCATTGCTGGAACTTCAGATGCTACAAGCGGAGGGCCATCTG
GGTCTGCTCAGGTTATCGACGGTAAAAGGGACAAAATTGTCCTCCTTAAAGGAAGAGCGA
GGGTTGATTCCAATCAGTCTGTGCCCCCGTCGAGAAATACACCTCCATCAACTTCTAGAC
AAGACCAGCGAAATGAGGCCAGTGGCAGAATTATCAAGACTATACTTTCAAACAAGGAAG
GACGCCATGCAATAGCATCTCAACATGAGCAAGAAGGTCACATAATTAGTGCCGAGAAGG
ATAAGAGGCCACCACGGGCTCCAAACTCGCGTTCCACTGCAAAAGATCAGATTGTTGAAA
ATGCTGAGAAAAACCATTATGATGACAAGCATAATCATGTGCATGGTTCTGGACCCATTG
GTGAGAAGATTGAAAGACATGCCAGAAATAGAGATAGGCCTGACCGAGGTGTTTGGGCCC
CTCGTCGCTATGACAAGTCTGCATCAGGAGGCGGTGCGCAAGCCTCATTGTCTGAGTTCC
CGCTAATGCAGTCACACTCTATGGACAATGTATCTCAGCAAGTAGATGGCCATGGAGAGC
GAAAAATAGACACAAGGGGTCCTGGTGGCCGCGGTGGCCTTGTGGAGAATGGAAACAGGC
ACCCCAACCGCCGTGGTCCGCCACGTGGGCCGAAGGAGATGGAAATCCCTCCTATTGCAT
CTGATGGAAAGCCTTCGAAGAGGGGCCCTGCTAGCTATGTGGCTCATGAGAGACAAGTAT
GGGTTCAGAAGTCAAGTTCAGGATCGTGAGTTTGTCCACCAATGATACTTTCATCAAAAT
AGATGTTGCAAGTTGTGGAGAAGTCTCTGGATTTTGCGGCTCATTCTGATTGTGAATGAA
ATGACTGTTGGTGAGATGGTTCTGTGAAGTGCAATTCCAGATTTGTCAACGGAAGTCTCA
GCTATAGCTGAAAAAGCAGCTCTTTGATTTGATTCACAGAATCACAGCAATAGTGAAGTA
ACATAACCCACCAGTAGGTAGCTCTCCATCACTTTGGGTGAGATTTGATTTTGGACCCAA
GGGTGCTATATCTGGAGGGACGGATGGAAATTAGGCTGGCATCAATACCTCGAGACAGTG
GTCACATATTTCCAAGACCCCTGGAGGCTATACACAAACCCGACGATTCATCAGTGATGG
ATGTACATATCTCTAGAGAAAGAAGAGGTCTGGCTCTGATTGCTGTTTACAGGTTAGAGG
TGCCATGTATCTACAAAGAGATAAGAGTTACCAGACTACCCAGTTTGCTAAATAAAGGTG
AATTTTTAGTTAGTTGATTATGAGAACCCCTGTATCCCGGCGGCTGCAGTTGCAGTCAGT
AAGACCGAAGTTACCGTGGAGTGCAAAGTGACAGCACTATCATGTTTTATGCTCCAGGTT
GAATGGAATGTGAGGCTATTTTGCTTGCTGATGTTGTGTTTTCTACTGTGACGTCACTCA
CCATATAAGTTTTTTTGGGGTTACGTTAAGAATTATATGCATGGTTATGGTGTACGCCAT
CAAAGGTGGTTGCTGTTTTTATTATCAGCAACAGATCTGCCTATGGGTCGTGCGCGCACT
GATCGGAGGAGGCAAAGTTCTCTTATTCTTGTAAGGGGAATTAGATCGTTCAATTAAACT
ACAAAGTCGCTGGTTAACTACTTACAATGCAGCTGGGATCAATTTCTTCCCAAGAATAGT
CATACTTAGCGAGTTTGTCAGCAACACCATAACCATGCCTATTGAAAGGGAACGAAGAAG
AAACAGGAAAAGGGAGTTCGGACTGTTACTTCGCCTAATATTGACCGTCCTGGTCCATCA
AAAACCACTTTTCCCTTCCGCTCACCTGGTCGAGGATGGCCCTGTTGCATGTCTGGCTGA
ACACATTTCCTTGCCGCATTCAAATGTCTAACTTGCGTGGAAG



Protein Sequence (500 aa)

>BART1_0-u12547.003 500 150831_barley_pseudomolecules
MKDPAHRTKVVLRRLPPAIAQQAVVDQVDARFAGRYDWARFRPGNASQKNHRYSRLYLNF
KSPEDVVEFAEFFNGHVFVNEKGAQFKALVEYAPSQQVPKSNIKKDARQGTITKDPEYLE
FLELISKPTEHLPSAEIQLERKEAERAAAGKEPPVITPLMVYVRQQRAAKSMAQRSVSSR
LSRKVAGVVTSSSSPSKRSSERRRASTSTQYVVRDNAKEKPTYILAPKRDDHTQREKIIA
GTSDATSGGPSGSAQVIDGKRDKIVLLKGRARVDSNQSVPPSRNTPPSTSRQDQRNEASG
RIIKTILSNKEGRHAIASQHEQEGHIISAEKDKRPPRAPNSRSTAKDQIVENAEKNHYDD
KHNHVHGSGPIGEKIERHARNRDRPDRGVWAPRRYDKSASGGGAQASLSEFPLMQSHSMD
NVSQQVDGHGERKIDTRGPGGRGGLVENGNRHPNRRGPPRGPKEMEIPPIASDGKPSKRG
PASYVAHERQVWVQKSSSGS