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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatattgtaaagtcctagccctgattgtttggaaggacaatactatgataaataaaaaaatatcaatttgtcttctaagctgttttttcctcaaa...

Basic information

species Zea mays
transcript GRMZM5G862959_T01
intron # 3
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|211484297|gb|FL254347.1|FL254347
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|4753396|gb|AI657306.1|AI657306
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211337492|gb|FL098066.1|FL098066
EST:     TTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: TTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTG-AGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|88753184|gb|DY537325.1|DY537325
EST:     CTTCGTGGTTTATATGCCCGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGA
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGA
EST: gi|148974314|gb|EE025087.2|EE025087
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|29944945|gb|CB815389.1|CB815389
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211484295|gb|FL254345.1|FL254345
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTAYTAGATGGTTTGTTGCAATCTGGA
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGA
EST: gi|31358058|gb|CD442415.1|CD442415
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTCGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211484293|gb|FL254343.1|FL254343
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211337495|gb|FL098069.1|FL098069
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAAATCTGGAG
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAA-TCTGGAG
EST: gi|211484294|gb|FL254344.1|FL254344
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211487166|gb|FL254349.1|FL254349
EST:     ACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: ACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|50326336|gb|CO521462.1|CO521462
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211337493|gb|FL098067.1|FL098067
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTACTAGATGGTTTGTTGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGC
EST: gi|211484292|gb|FL254342.1|FL254342
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211384387|gb|FL373404.1|FL373404
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211484291|gb|FL254341.1|FL254341
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|32914541|gb|CF019353.1|CF019353
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211337491|gb|FL098065.1|FL098065
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|28873324|gb|CB329328.1|CB329328
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211484296|gb|FL254346.1|FL254346
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211043059|gb|FL422974.1|FL422974
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|93012241|gb|EB637761.1|EB637761
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGC
EST: gi|211337490|gb|FL098064.1|FL098064
EST:     CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG                         TGCCTCAAATGCTTTGATTGGAT
genomic: CTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGAT

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), 48 (downstream exon)
Score: 105

CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 130

CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatat ... cttcttgcagTGCCTCAAATGCTTTGATTGGATTATTAGATGGTTTGTTGCAATCTGGAGCTTCAACTGCACAAAAGAAAAAGATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAGgtaaatatattgtaaagtcctagccctgattgtttggaaggacaatactatgataaataaaaaaatatcaatttgtcttctaagctgttttttcctcaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT