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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcccaatgatttggacgacttatgttatggttctgctagatgtcatttgatttgcctcattaggtaaacataaaaattgttttatgtgtggtgtgtaacttcttgttttcatgcgttgatcag

Basic information

species Zea mays
transcript GRMZM2G163193_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163193_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g43350.1 (Oryza sativa), 5'ss of exon 12
AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtga----tctgcccaatgatttggacgacttatgttat---ggttctgctagatgtcatttgatttgcctcattaggt-aaacataaaaattgttttatgtgtggtgtgtaacttcttgttttcatgcgttgatcag
 ||||||||||||| ||| | ||  | || || || || |||||||||||| | |||||||||||| |||||||||||||||| |||||||||||||||||| |       | ||||    |  |    | ||||||||   || ||| ||   | | ||  | ||||| ||||||| | ||| || |||| ||||| |  | ||     ||||  |||  ||   | |     ||||
CGGGAAGTAAAAGCCCTTCTTCAATCAGCCCTTGATGTCGCTCTTTCAGTTGTCCGTGCTAATCCTACAGTTTTGGAAGGCCTTGGAGCATATTTAGAAGgtaaaaaactagaccaaattatcaggttgcatatgttattgtggctctcctttctatgatgggttttgcttcattagattaaaaatgaaaactgtttaacctatg---cataacggctttcttctctaccccattcag
















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|67029785|gb|CO458534.1|CO458534
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
EST: gi|78121515|gb|DV539899.1|DV539899
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
EST: gi|71449715|gb|DR830765.1|DR830765
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
EST: gi|67033989|gb|CO462738.1|CO462738
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
EST: gi|13562289|gb|BG550509.1|BG550509
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGATTATTGTTCTAAAGTCAGTT
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTG-GCTAAAGTCAGTT
EST: gi|71329683|gb|DR801566.1|DR801566
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTCGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
EST: gi|13558170|gb|BG549526.1|BG549526
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGTGGTTTTTTGTAGAGTGGCTAAAGTCAGTT
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGG-AACTTGAAGAGTGGCTAAAGTCAGTT
EST: gi|211228739|gb|FL103757.1|FL103757
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
EST: gi|13558169|gb|BG549525.1|BG549525
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
EST: gi|101384111|gb|EB814110.1|EB814110
EST:     TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAG                         AGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG
genomic: TATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTG

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: 46 (upstream exon), 49 (downstream exon)
Score: 76

AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTGTTGCATCAAAAGAGTTGACCTCTTTTATCAGAGGACAGCAAGAGCAAGT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 173

AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTGTTGCATCAAAAGAGTTGACCTCTTTTATCAGAGGACAGCAAGAGCAAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 260

AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTGTTGCATCAAAAGAGTTGACCTCTTTTATCAGAGGACAGCAAGAGCAAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcc ... cgttgatcagAGAATGAAAAGGTTGAAGGCGAGGAACTTGAAGAGTGGCTAAAGTCAGTTGTTGCATCAAAAGAGTTGACCTCTTTTATCAGAGGACAGCAAGAGCAAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGAAGTAAAAGCGCTTTTACAGACGGCACTGGAAGTAGCTCTTTCAGTTATTCGTGCTAATCCTGCAGTTTTGGAAGGCCTCGGAGCATATTTAGAAGgtgatctgcccaatgatttggacgacttatgttatggttctgctagatgtcatttgatttgcctcattaggtaaacataaaaattgttttatgtgtggtgtgtaacttcttgttttcatgcgttgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA