Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u18453.002

ChromosomeExonStartStopDirection
chr3H14755724947557102+
chr3H24755762847557557+
chr3H34755873247558463+
chr3H44755920647559088+
chr3H54755949547559319+
chr3H64755984947559802+
chr3H74756008447560020+
chr3H84756051147560173+


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
morexEMB0.8380840.7709312.42238
morexETI2.46682.005734.75839
morexLEA2.116611.768951.40382
morexEPI1.3065902.99164
morexROO0.4007120.7657110.849925
morexROO20.7154520.9468431.31605
morexNOD3.727112.375028.59879
morexRAC2.778252.107491.15242
morexINF13.810883.752572.81543
morexINF25.733095.831714.75958
morexCAR55.747276.059024.68664
morexCAR152.199282.123781.0837
morexLEM4.462634.429572.94551
morexLOD3.880365.238042.86673
morexPAL1.43452.516743.1004
morexSEN1.3857300.386467



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os10g41730.1 +2 1e-94 283 143/179 (80%) protein|expressed protein
TAIR PP10 AT5G43822 @ ARAPORT
AT5G43822.1 @ TAIR		 +2 1e-42 148 77/180 (43%) Symbols: | Pentatricopeptide repeat (PPR) superfamily protein | chr5:17620830-17621868 FORWARD LENGTH=195
BRACH PP3 Bradi3g33790.2.p +2 4e-109 319 156/179 (87%) pacid=32818824 transcript=Bradi3g33790.2 locus=Bradi3g33790 ID=Bradi3g33790.2.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 (1238 bp)

>BART1_0-u18453.002 1238 150831_barley_pseudomolecules
CTTGGACGTTTGCCCTCTTACAGGTCGGGCCCGCTTGAAATCCCGGTTTTACCCCCGGCC
AGCCTCCCTGCTCTTCCTCGAGGCGACACACCGGTGGACGGCGACGGTGGTAATCGACGG
CGGAGGCTCCCTCCCGGCAACAACGACAACCATTGGAAGCTAGGGTTCATCACTGCACAT
TGGGGAATTTCGTGTGAAGGACCACTTCTTCATTCAACATGTTGACCTGAGCCCAGCCTA
TCATACGTGCCTCGTTCTCAGCAGCTGCAGACGTTCCCTAAGAAAATAGGCAAGCACTGC
CGAGAAATCGATCGAGGACCGGGGTTGCTAAGGGAAACGAGATGAGCGGTTGATCGGGAT
GGAGGTTGTGGTGCGGAAGATGCAGCAGCGGGTGAGGAAGGCACGGGAGGAGACGGAGCG
ATGGGATGACCTCAACTCCCGCCTCCTGTCCCAGTTCTCCAATGCTGCCGCCATCATCAC
CCGCCTTCTGGTACTTGGAGATGCTAAAAATCATGGTATCCTGCGGTGTGTGCCCAACAT
CAGGGAGGATCTCTTGGGGGCACAGATGAGGAGCCTGGAGCTCATATTTGTTTCAATGAG
GGAGACTCTGGAGGAGTTCAGTGGCATTGCCAAAGGTTTGAGCAAGGTACTGCGCGATGC
TAATCAGATGGTGAGGGGTGGATTGGCACTCACTGGGAAACAATTGCAGTTACAAGTGGG
AATTTTGCCAACTATTGCAGACTGCTTGGGTGGGCTACAAACACTGTCTGAAATGCACCA
GGCTGAGTATGCGCTAAAATCATCAATCATCTCTTTGTTGACATGGAAAAGCAGTTCAAG
TGAAATCGCTGCAATGCGTCAACTCTTGGTAGACCAACCAAACATACCGAAAGATGAAGT
GCAATCTGTCTTCGACATTATATTTGCAGATGAAATTTGCTAAGTTGAGCATGCATCCTA
CTATTGGAAGCCCTATTGCCAAGACATGTTGAAGCAACTGTATTTTGATCTACTCCTTCC
GTTCATAAATATAAGCTTTTCTGACCTTTCTGTGAATCGGATATATATAGACACGTTTTA
GTGTCTTTGTTCACTCATTTCACTCGTGTATGTAGTCCATATTGAAATATCCAAACCATG
GTATATTTGTGAACGGAGGGAGTACTTTCTTATCTGAACAAAGTGTTGAGTAAATAGGCA
ATTTTCCGAGTACATTAATCCACAAAATAATAACTAGC



Protein Sequence (194 aa)

>BART1_0-u18453.002 194 150831_barley_pseudomolecules
MEVVVRKMQQRVRKAREETERWDDLNSRLLSQFSNAAAIITRLLVLGDAKNHGILRCVPN
IREDLLGAQMRSLELIFVSMRETLEEFSGIAKGLSKVLRDANQMVRGGLALTGKQLQLQV
GILPTIADCLGGLQTLSEMHQAEYALKSSIISLLTWKSSSSEIAAMRQLLVDQPNIPKDE
VQSVFDIIFADEIC