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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacttttatatgattttctgggttacagtatccttgatttgttttcagcgttgcttgttgctacttgctatttgcttataatatccctacaatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGGTTTGTCCAACATTATTGTCGTGGACAATCTGCCAGTTGTTCCTCCAGAA

Basic information

species Zea mays
transcript GRMZM2G174757_T01
intron # 1
splice site 3'
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|211183847|gb|FL114915.1|FL114915
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211181446|gb|FL114903.1|FL114903
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACRAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211181447|gb|FL114904.1|FL114904
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211183853|gb|FL114921.1|FL114921
EST:     GAWCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211183855|gb|FL114923.1|FL114923
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211183848|gb|FL114916.1|FL114916
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|89759553|gb|DY688345.1|DY688345
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGAATCGTCAG                         TGATGACCAGGAGGTACTTCGTGGTGAGGATCTTCCCGAACTT
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTT
EST: gi|211181449|gb|FL114906.1|FL114906
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211181452|gb|FL114909.1|FL114909
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211183845|gb|FL114913.1|FL114913
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211181455|gb|FL114912.1|FL114912
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|78085595|gb|DV513988.1|DV513988
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211183849|gb|FL114917.1|FL114917
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|149098249|gb|EE184215.2|EE184215
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|9952026|gb|BE638609.1|BE638609
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211020785|gb|FL433473.1|FL433473
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211181453|gb|FL114910.1|FL114910
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGAGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211183850|gb|FL114918.1|FL114918
EST:     ATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCNRG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGG
genomic: ATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCA-Ggtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGG
EST: gi|211181448|gb|FL114905.1|FL114905
EST:     GATCTGGACTCCATCACCCTCCCGGCCGNCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211183852|gb|FL114920.1|FL114920
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|149079566|gb|EE168554.2|EE168554
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|31441047|gb|CD510478.1|CD510478
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|148971737|gb|EE022470.2|EE022470
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
EST: gi|211181443|gb|FL114900.1|FL114900
EST:     GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAG                         TGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG
genomic: GATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGG

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: 662

AGGGCATCGAGGCGCGGGCGCGGGATCTCGGGGTGGACCTCTCCGCTGTCGATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGGTTTGTCCAACATTATTGTCGTGGACAATCTGCCAGTTGTTCCTCCAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 414

AGGGCATCGAGGCGCGGGCGCGGGATCTCGGGGTGGACCTCTCCGCTGTCGATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGGTTTGTCCAACATTATTGTCGTGGACAATCTGCCAGTTGTTCCTCCAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 459

AGGGCATCGAGGCGCGGGCGCGGGATCTCGGGGTGGACCTCTCCGCTGTCGATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGGTTTGTCCAACATTATTGTCGTGGACAATCTGCCAGTTGTTCCTCCAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 471

AGGGCATCGAGGCGCGGGCGCGGGATCTCGGGGTGGACCTCTCCGCTGTCGATCTGGACTCCATCACCCTCCCGGCCGGCGAGGACTTCGGCATCGTCAGgtagacgcac ... caatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGGTTTGTCCAACATTATTGTCGTGGACAATCTGCCAGTTGTTCCTCCAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagcgttgcttgttgctacttgctatttgcttataatatccctacaatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGGTTTGTCCAACATTATTGTCGTGGACAATCTGCCAGTTGTTCCTCCAGAA
                                       tccctac  CT-rich tract
                        tatttgcttataatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacttttatatgattttctgggttacagtatccttgatttgttttcagcgttgcttgttgctacttgctatttgcttataatatccctacaatttgcagTGATGACGAGGAGGTACTTCGTGGTGAGGATCTTCCAGAACTTGAAATGGGTTTGTCCAACATTATTGTCGTGGACAATCTGCCAGTTGTTCCTCCAGAA

- - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - -cgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgctt