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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCCCGGGGGCCGGAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCTAGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgctccttctcctggttagaaattgtttaatttgataaacgactatgacccttggttccgcgtaaggtatggggggctggccctacatcagac...

Basic information

species Zea mays
transcript GRMZM2G028369_T01
intron # 1
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211029810|gb|FL058988.1|FL058988
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211092233|gb|FL378442.1|FL378442
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211490416|gb|FL381909.1|FL381909
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027365|gb|FL058974.1|FL058974
EST:     AGAAACAAAGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027362|gb|FL058971.1|FL058971
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211029808|gb|FL058986.1|FL058986
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027366|gb|FL058975.1|FL058975
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|9824918|gb|BE575015.1|BE575015
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027371|gb|FL058980.1|FL058980
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027370|gb|FL058979.1|FL058979
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211029814|gb|FL058992.1|FL058992
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|149067525|gb|EE157731.2|EE157731
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211024914|gb|FL058965.1|FL058965
EST:     AGAAACAAGGGGCTTCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211029809|gb|FL058987.1|FL058987
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|71449541|gb|DR830591.1|DR830591
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|148987695|gb|EE031582.2|EE031582
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027360|gb|FL058969.1|FL058969
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|91872761|gb|EB402718.1|EB402718
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211148548|gb|FL374616.1|FL374616
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211488629|gb|FL426432.1|FL426432
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211387290|gb|FL388817.1|FL388817
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211063320|gb|FL403461.1|FL403461
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211029804|gb|FL058982.1|FL058982
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|78104614|gb|DV523032.1|DV523032
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|71447644|gb|DR828694.1|DR828694
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211029806|gb|FL058984.1|FL058984
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGAC
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCT-AAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGAC
EST: gi|211027363|gb|FL058972.1|FL058972
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGWGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|32926797|gb|CF031609.1|CF031609
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211442013|gb|FL419339.1|FL419339
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027358|gb|FL058967.1|FL058967
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027357|gb|FL058966.1|FL058966
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211029812|gb|FL058990.1|FL058990
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|32849098|gb|CD988779.1|CD988779
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027359|gb|FL058968.1|FL058968
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|89764470|gb|DY691264.1|DY691264
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
EST: gi|211027367|gb|FL058976.1|FL058976
EST:     AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAA                         GGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA
genomic: AGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

TCGCCCGGGGGCCGGAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCTAGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

TCGCCCGGGGGCCGGAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCTAGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 227

TCGCCCGGGGGCCGGAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCTAGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 249

TCGCCCGGGGGCCGGAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCTAGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgc ... cttttattagGGAAGAGAGGGTTGATCGAAGTGAAATATTGACATTGGATAGCATTAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGCCCGGGGGCCGGAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCTAGAAACAAGGGGCTCCGCGCGGCCAACAACTCCGCGACGCCCGTGGCTAAgtacgaacgctccttctcctggttagaaattgtttaatttgataaacgactatgacccttggttccgcgtaaggtatggggggctggccctacatcagac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctccttc