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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCCCGGGGGCCGCAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCCAGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacactccttatcctgcttagaaattgtttggtttaataaacaactgtgccccttggttccgtgtaaggtatgcggggttaatcctagatccatg...

Basic information

species Zea mays
transcript GRMZM2G124365_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|67040651|gb|CO466906.1|CO466906
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211128223|gb|FL382946.1|FL382946
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|71304463|gb|DR788345.1|DR788345
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842618|gb|CD982299.1|CD982299
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842597|gb|CD982278.1|CD982278
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|67040128|gb|CO466383.1|CO466383
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842683|gb|CD982364.1|CD982364
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|67041520|gb|CO467775.1|CO467775
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211042173|gb|FL385501.1|FL385501
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842669|gb|CD982350.1|CD982350
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211323552|gb|FL394714.1|FL394714
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGMAAGTGACATATTGACATTGGATAGCATCAGAC
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCG-AAGTGACATATTGACATTGGATAGCATCAGAC
EST: gi|32842206|gb|CD981887.1|CD981887
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211131047|gb|FL391845.1|FL391845
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842514|gb|CD982195.1|CD982195
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211326342|gb|FL425003.1|FL425003
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842415|gb|CD982096.1|CD982096
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842444|gb|CD982125.1|CD982125
EST:     GGAACAAGGGGCTCCGCGCGGCCAACAAGCTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: GGAACAAGGGGCTCCGCGCGGCCAACAA-CTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|148931381|gb|EC874300.2|EC874300
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|148996150|gb|EE035419.2|EE035419
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|149077332|gb|EE166011.2|EE166011
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842790|gb|CD982471.1|CD982471
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842552|gb|CD982233.1|CD982233
EST:     AGGAACAAGGGGCTCCGCGCGGGCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842439|gb|CD982120.1|CD982120
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211236776|gb|FL420045.1|FL420045
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211222127|gb|FL422630.1|FL422630
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842376|gb|CD982057.1|CD982057
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842412|gb|CD982093.1|CD982093
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|37422138|gb|CF648774.1|CF648774
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|89763811|gb|DY690849.1|DY690849
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842408|gb|CD982089.1|CD982089
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|32842587|gb|CD982268.1|CD982268
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211217423|gb|FL401820.1|FL401820
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
EST: gi|211035045|gb|FL415129.1|FL415129
EST:     AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAA                         GGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA
genomic: AGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACA

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), 45 (downstream exon)
Score: 92

TCGCCCGGGGGCCGCAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCCAGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 491

TCGCCCGGGGGCCGCAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCCAGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 610

TCGCCCGGGGGCCGCAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCCAGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1303

TCGCCCGGGGGCCGCAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCCAGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacac ... cttttattagGGTAGAGAGGGTTGATCGAAGTGACATATTGACATTGGATAGCATCAGACAAGTTTTGATTAGACTAGAAGACAGCATCATATTTGGCCTTTTGGAGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGCCCGGGGGCCGCAGGGTACGAGCCGCGTTGCCTTCGGACCAGCGCCCAGGAACAAGGGGCTCCGCGCGGCCAACAACTCCGCAACGCCCATAGCTAAgtacgaacactccttatcctgcttagaaattgtttggtttaataaacaactgtgccccttggttccgtgtaaggtatgcggggttaatcctagatccatg

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