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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagctaacggatccatacatatatgcaacaatgtgtgagttcagcagctagttcgtgttactcaggggtgttcaatttaaaccacttgtgccaa...

Basic information

species Zea mays
transcript GRMZM2G092497_T04
intron # 2
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|78088679|gb|DV517072.1|DV517072
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|78109829|gb|DV528245.1|DV528245
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|28873635|gb|CB329598.1|CB329598
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|211528668|gb|FL445662.1|FL445662
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|71325873|gb|DR799620.1|DR799620
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|76913046|gb|DV164985.1|DV164985
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|91873568|gb|EB403525.1|EB403525
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|71447185|gb|DR828235.1|DR828235
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|74238865|gb|DT646779.1|DT646779
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|149074707|gb|EE163131.2|EE163131
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGGTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
EST: gi|89762158|gb|DY689885.1|DY689885
EST:     CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGG                         GTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG
genomic: CATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAG

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 36

TGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAGTATGTGGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 66

TGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAGTATGTGGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 70

TGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagc ... tggttttaagGTTGCTAATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAGTATGTGGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGTAACGGGGAGCAGACAGTGAGCTTCAACGCTGCTGGTGCTGGTTCATCAGCTCTGGCAGCGACGAACACTGATGCTCCTGGCCCATCGACACGGgtaagccagctaacggatccatacatatatgcaacaatgtgtgagttcagcagctagttcgtgttactcaggggtgttcaatttaaaccacttgtgccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC