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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGAATTTGCCCGCGGAGGGTTCGGATTCAGCGCCAGCGTCAGTGGTGGCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctatcctgtccggatttctcctcgtgctgcatgggtcgcttcaaaatggggaataattgttggctacttgatatttcccaacaacgattcgcgc...

Basic information

species Zea mays
transcript GRMZM2G122064_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|32827677|gb|CD967355.1|CD967355
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTA
EST: gi|211350744|gb|FL045061.1|FL045061
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
EST: gi|71446024|gb|DR827074.1|DR827074
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
EST: gi|32803023|gb|CD955259.1|CD955259
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGGATTA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTA
EST: gi|32789399|gb|CD941635.1|CD941635
EST:     GTAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTA
EST: gi|32805160|gb|CD957396.1|CD957396
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTA
EST: gi|211350743|gb|FL045060.1|FL045060
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
EST: gi|148954876|gb|EC900353.2|EC900353
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
EST: gi|149112489|gb|EE295360.2|EE295360
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
EST: gi|32805175|gb|CD957411.1|CD957411
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTA
EST: gi|32790998|gb|CD943234.1|CD943234
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTA
EST: gi|211350745|gb|FL045062.1|FL045062
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGA
EST: gi|148967009|gb|EE018161.2|EE018161
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
EST: gi|32805445|gb|CD957679.1|CD957679
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTA
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTA
EST: gi|148965580|gb|EE016411.2|EE016411
EST:     GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATG                         TACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG
genomic: GCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAG

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: 147

CGGCGAATTTGCCCGCGGAGGGTTCGGATTCAGCGCCAGCGTCAGTGGTGGCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAGGAAACGGGCGCTTACTTGTCAACACTGGAATCGTCTATTTTCAGCAAAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 96

CGGCGAATTTGCCCGCGGAGGGTTCGGATTCAGCGCCAGCGTCAGTGGTGGCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAGGAAACGGGCGCTTACTTGTCAACACTGGAATCGTCTATTTTCAGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

CGGCGAATTTGCCCGCGGAGGGTTCGGATTCAGCGCCAGCGTCAGTGGTGGCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAGGAAACGGGCGCTTACTTGTCAACACTGGAATCGTCTATTTTCAGCAAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

CGGCGAATTTGCCCGCGGAGGGTTCGGATTCAGCGCCAGCGTCAGTGGTGGCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctat ... tcttctctagTACATTTCATTCTAGGGGTGGAATTAAATCTCCGTGGTCTCGAAGAAAAAGGAAACGGGCGCTTACTTGTCAACACTGGAATCGTCTATTTTCAGCAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCGAATTTGCCCGCGGAGGGTTCGGATTCAGCGCCAGCGTCAGTGGTGGCAGCTTCCTCGTCGCCCTCGCTGGCTGCTTCGTCTCCGAACATGGAATGgtggggctatcctgtccggatttctcctcgtgctgcatgggtcgcttcaaaatggggaataattgttggctacttgatatttcccaacaacgattcgcgc

- - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA