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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtcttctgttctttgcactgattgacggctatcagtggatcttaaatttggacttattctcttattgtgttgcaattaattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA

Basic information

species Zea mays
transcript GRMZM2G131998_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131998_T04 (Zea mays), 3'ss of exon 4
lower sequence: AT1G03110.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtcttctgttctt-tgcactgattgacggctatcagtggatcttaaatttggacttattctcttattgtgttgcaattaattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA
  ||   ||  |||  | |||| ||  ||   | ||| |   | |     |  || |  |  | |  |  |  ||   ||    |  ||||| ||  | || || ||||| |||||| ||||||| |||||||||||||| ||||| ||||| ||| ||||
--gtaagctagtctaatccactaatgcacaa-tgtca-tacctttcttgctcagattggtcttatagtgattctgt--ttgccatcacagGTGACTGTTTTTCCCAAGAAGCCTCTAGAAGGGGCTCATGAAATACAGAGTTTTTGTCTTGGACATTCAGA
















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|78091377|gb|DV519751.1|DV519751
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|87156923|gb|DY401712.1|DY401712
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|89761079|gb|DY689237.1|DY689237
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|89249366|gb|DY621152.1|DY621152
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAAC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|148936297|gb|EC880380.2|EC880380
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|71437750|gb|DR818800.1|DR818800
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|148959295|gb|EE010708.2|EE010708
EST:     CAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTTCAAA-TACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCAATGAA-TACAGAG
genomic: CAGATGGACGGTTCATTGCTACTGCTGATAGGGACTT-CAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCA-TGAAATACAGAG
EST: gi|148945698|gb|EC890971.2|EC890971
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|148973467|gb|EE024565.2|EE024565
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|149081963|gb|EE171128.2|EE171128
EST:     CCGGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGGAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|78106892|gb|DV525310.1|DV525310
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|78081795|gb|DV510207.1|DV510207
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|20811129|gb|BQ295607.1|BQ295607
EST:     CCAGATGGACGGNTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATC
EST: gi|149111910|gb|EE191066.2|EE191066
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|89759711|gb|DY688443.1|DY688443
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|148964964|gb|EE015811.2|EE015811
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         GTCACATTATTCCC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCC
EST: gi|76017216|gb|DT944386.1|DT944386
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|50331437|gb|CO526563.1|CO526563
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
EST: gi|71771570|gb|DR969507.1|DR969507
EST:     CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGT                         --CACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC
genomic: CCAGATGGACGGTTCATTGCTACTGCTGATAGGGACTTCAAAATACGAGTgtgtcttctg ... aattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtggatcttaaatttggacttattctcttattgtgttgcaattaattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA
                                         aattaat  putative branch site (score: 3)
                                     ttgcaattaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtcttctgttctttgcactgattgacggctatcagtggatcttaaatttggacttattctcttattgtgttgcaattaattttgcagGTCACATTATTCCCAAAGAATCCTCTAAAAGGGGCCCATGAAATACAGAGCTTTTGCCTTGGGCATACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT