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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcactcttgtctattggttaataattgatgcttcattgatatcatcacaaagttttctattgctatatgtgcaacttcagttgtgttgtccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCTGATGTTCAGATATCTAATAAGTG

Basic information

species Zea mays
transcript GRMZM5G886883_T03
intron # 5
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|71305066|gb|DR788670.1|DR788670
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|78109684|gb|DV528100.1|DV528100
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|148947131|gb|EC892444.2|EC892444
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|93014964|gb|EB640484.1|EB640484
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|149000423|gb|EE037594.2|EE037594
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|148992844|gb|EE033671.2|EE033671
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|148982611|gb|EE028409.2|EE028409
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATC
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATC
EST: gi|149088271|gb|EE177365.2|EE177365
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|148996312|gb|EE035595.2|EE035595
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|149000477|gb|EE037653.2|EE037653
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|67031282|gb|CO460031.1|CO460031
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTANAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|71767172|gb|DR965109.1|DR965109
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|60339883|gb|DN206856.1|DN206856
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
EST: gi|149078105|gb|EE166854.2|EE166854
EST:     GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAG                         GATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT
genomic: GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCT

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: 44 (upstream exon), 46 (downstream exon)
Score: 62

GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCTGATGTTCAGATATCTAATAAGTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 85

GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCTGATGTTCAGATATCTAATAAGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 103

GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCTGATGTTCAGATATCTAATAAGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 86

GTGGAACCTTGCCAAAAATAAGGCCTCACCCTTGGAGATTAAAAAGgtgggtaacc ... tccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCTGATGTTCAGATATCTAATAAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacaaagttttctattgctatatgtgcaacttcagttgtgttgtccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCTGATGTTCAGATATCTAATAAGTG
                                          ttgtccttttc  CT-rich tract
         ttttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcactcttgtctattggttaataattgatgcttcattgatatcatcacaaagttttctattgctatatgtgcaacttcagttgtgttgtccttttcagGATGTAGTTCTGTTGGATGACGATGATGATATAGAGCCTGCTAGATCAGCTGATGTTCAGATATCTAATAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
-tgcactc
- - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - -atcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttg