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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacatcaaattccttggtttgtggaggccacaggatgataatgcctgatttgaggtacaagacttcaagatttactgatgttatccttacattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATTGGCTGGAATAATACAATTGGTCAACAAAGGTGTTTGCTCAACTATGAAT

Basic information

species Zea mays
transcript GRMZM2G048804_T02
intron # 11
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|31558703|gb|CD527915.1|CD527915
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|94472950|gb|EB701908.1|EB701908
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATTTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|12968751|gb|BG265697.1|BG265697
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|113704317|gb|EE681821.1|EE681821
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|40335164|gb|CK369234.1|CK369234
EST:     CTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: CTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|37379196|gb|CF626330.1|CF626330
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|5791304|gb|AI978096.1|AI978096
EST:     ATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTTCAAG
genomic: ATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTT-CAAG
EST: gi|50339821|gb|CO534947.1|CO534947
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|33467111|gb|CF244160.1|CF244160
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATTTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|5005582|gb|AI711644.1|AI711644
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|5895669|gb|AW036915.1|AW036915
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|71773196|gb|DR971109.1|DR971109
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|211094046|gb|FL457289.1|FL457289
EST:     GTATACAACGCCAGAACCCTTTAGAAGGACTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|74236760|gb|DT644674.1|DT644674
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|211155842|gb|FL114458.1|FL114458
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|32911197|gb|CF016009.1|CF016009
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|24764009|gb|CA399178.1|CA399178
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|78021285|gb|DV489672.1|DV489672
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
EST: gi|113702828|gb|EE680332.1|EE680332
EST:     ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAG                         ATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT
genomic: ATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATT

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: 45 (upstream exon), 47 (downstream exon)
Score: 102

TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATTGGCTGGAATAATACAATTGGTCAACAAAGGTGTTTGCTCAACTATGAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 105

TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATTGGCTGGAATAATACAATTGGTCAACAAAGGTGTTTGCTCAACTATGAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 118

TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATTGGCTGGAATAATACAATTGGTCAACAAAGGTGTTTGCTCAACTATGAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 133

TTACTGGATGAAATAGCTGCAAAATTTTACAATATACAACGCCAGAACCCTTTAGAAGGCCTTTTCAGCGAAATGTTCAAGgtaagcctta ... cattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATTGGCTGGAATAATACAATTGGTCAACAAAGGTGTTTGCTCAACTATGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatttgaggtacaagacttcaagatttactgatgttatccttacattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATTGGCTGGAATAATACAATTGGTCAACAAAGGTGTTTGCTCAACTATGAAT
                                       tccttac  putative branch site (score: 133)
                                       tccttac  CT-rich tract
                      aagattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacatcaaattccttggtttgtggaggccacaggatgataatgcctgatttgaggtacaagacttcaagatttactgatgttatccttacattctgcagATATAATGCACGAGAAAAGAATTTTATGTCGATGCTTTCATCTAAACCATTGGCTGGAATAATACAATTGGTCAACAAAGGTGTTTGCTCAACTATGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA