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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcggaggggtacaaatacaaaccattgttgttcactgttatcaacatttttgttcatgaagcctgttgatggacattggtctgtgttcttttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACTCATGTATGATGTGAAGACTGGCGGTATAGTGGTGCTACTCAAAGTTTGT

Basic information

species Zea mays
transcript GRMZM2G058560_T01
intron # 1
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|60397805|gb|DN230621.1|DN230621
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|76928090|gb|DV171482.1|DV171482
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|110517352|gb|EE021939.1|EE021939
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTTTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|211349463|gb|FK984272.1|FK984272
EST:     GARAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGACTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAA-CT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|78124680|gb|DV543064.1|DV543064
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTTTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|88754763|gb|DY538904.1|DY538904
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCCCCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|71450169|gb|DR831219.1|DR831219
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|60359287|gb|DN226260.1|DN226260
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|78091613|gb|DV519987.1|DV519987
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|30032053|gb|CB833904.1|CB833904
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|71757955|gb|DR955892.1|DR955892
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|89250462|gb|DY622248.1|DY622248
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTTTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|74246225|gb|DT654139.1|DT654139
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|74242741|gb|DT650655.1|DT650655
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|91055335|gb|EB165753.1|EB165753
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|193501829|gb|AM937962.1|AM937962
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGACTAATAACATCTTTAGGGGAGCTCACCAATGATCCGTGAGAA-CT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|148961427|gb|EE012169.2|EE012169
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTTTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|16377488|gb|BI991960.1|BI991960
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|193502479|gb|AM937801.1|AM937801
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGACTAATAACATCTTTAGGGGAGCTCACCAATGATCCGTGAGAA-CT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|193502898|gb|AM937548.1|AM937548
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGACTAATAACATCTTTAGGGGAGCTCACCAATGATCCGTGAGAA-CT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT
EST: gi|211070289|gb|FL462525.1|FL462525
EST:     GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATG                         GGAGGACTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAA-CT
genomic: GAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACT

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: 48 (upstream exon), 46 (downstream exon)
Score: 115

GGAAGAAAGTTAACAGTGGGCTGCTAAAGATGTACAAGGCTGAGGTGCTTGAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACTCATGTATGATGTGAAGACTGGCGGTATAGTGGTGCTACTCAAAGTTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GGAAGAAAGTTAACAGTGGGCTGCTAAAGATGTACAAGGCTGAGGTGCTTGAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACTCATGTATGATGTGAAGACTGGCGGTATAGTGGTGCTACTCAAAGTTTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98

GGAAGAAAGTTAACAGTGGGCTGCTAAAGATGTACAAGGCTGAGGTGCTTGAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACTCATGTATGATGTGAAGACTGGCGGTATAGTGGTGCTACTCAAAGTTTGT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 44

GGAAGAAAGTTAACAGTGGGCTGCTAAAGATGTACAAGGCTGAGGTGCTTGAGAAAGTACCGATCATGCAGCATTTCCTCTTTGGCTCACTAATCAAATGgtatgagttg ... tttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACTCATGTATGATGTGAAGACTGGCGGTATAGTGGTGCTACTCAAAGTTTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttgttcatgaagcctgttgatggacattggtctgtgttcttttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACTCATGTATGATGTGAAGACTGGCGGTATAGTGGTGCTACTCAAAGTTTGT
                   tgttgat  putative branch site (score: 44)
                                   tctgtgttcttttttt  putative PPT
                                         ttctttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcggaggggtacaaatacaaaccattgttgttcactgttatcaacatttttgttcatgaagcctgttgatggacattggtctgtgttcttttttttcagGGAGGATTAATAACATCTTTAGGGAAGCTCACCAATGATCCGTGAGAAACTCATGTATGATGTGAAGACTGGCGGTATAGTGGTGCTACTCAAAGTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - -gtacaaa
- - - - - - - - - caaacca
- - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgttg