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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggattcctgcaatgcctagcactgccacctgaatggattcctgcctaggtgaacttctgcaggtcattgatgtgagccattttatctttcttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAACCAACCAACCAATCTGACGAGCTTTAGATTCATCAAACAAATGAATCCAT

Basic information

species Zea mays
transcript GRMZM2G115757_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115757_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G21680.1 (Glycine max), 3'ss of exon 5
tggattcctgcaatgcctagcac-tgccacctgaatggattcctgcctaggtgaacttctgcaggtcattgatgtgagccattttat--ctttcttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAACCAACCAACCAATCTGACGAGCTTTAGATTCATCAAACAAATGAATCCAT
    ||||   |||   |||    |   || |   |  | |      |||   |    ||  |    ||| || |  ||   | |||  ||||   ||| ||||||| ||||| |||||||||||||| |||||||| |  || || |   ||        | ||    | ||    |     |   | |||||| ||   | 
---tttccattaatttttagtctgtattacttttttatactatatattagccaactaactatattatattaatatatgctcatatatgacttttaacttacagGTGGTGCAACACTCATATTTGACACTGAGCTTGTGGGAGTGAACGACAAAAGTTTAGGCGAAGAAAAAGAAAACTCCGAACTGTAGACAAATCAAAAGAA

upper sequence: GRMZM2G115757_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0260g00060.t01 (Vitis vinifera), 3'ss of exon 5
tggattcctgcaatgcctagca-ctgccacctgaatggattcctgcctaggtgaacttctgcaggtcattgatgtgagccattttatctttcttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAACCAACCAACCAATCTGACGAGCTTTAGATTCATC---AAACAAATGAATCCAT
||| |   |   | |  |  |  |   ||  | ||   ||   |  |      |  || |            | ||      | | |  |    ||||||||||||||||| || || |||||||| |||||||| ||||| |||||| || || | | |  | |  | |    | | | | | |   ||||| | |||     
tggctgttttataggtttgtcttccaacagttcaaccaatatatatcatcaaaatattatctgatgggacagtatggtatgatct-ttgtcaaccttgcagGTGGAGCAACACTTATCTTTGACACCGAGCTTGTTGCTGTGAATGGAAAAGCATCAAGCGGAGCCAAAGCAGATGACAGTGAGCTATAAACAGAGGAACA---
















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|32936362|gb|CF041181.1|CF041181
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|211211874|gb|FL151949.1|FL151949
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|213167545|gb|FM181750.1|FM181750
EST:     CCATCAAANNNNTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCATCAAA-GCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|211214433|gb|FL151952.1|FL151952
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|32932853|gb|CF037665.1|CF037665
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|211214432|gb|FL151951.1|FL151951
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|32909171|gb|CF013983.1|CF013983
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|32933739|gb|CF038551.1|CF038551
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|37388080|gb|CF631245.1|CF631245
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|32828559|gb|CD968237.1|CD968237
EST:     CTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|12968665|gb|BG265611.1|BG265611
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCCCCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|211343044|gb|FL472494.1|FL472494
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|32795582|gb|CD947818.1|CD947818
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|211343045|gb|FL472495.1|FL472495
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|33104467|gb|CF064427.1|CF064427
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|6227228|gb|AW155827.1|AW155827
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|32794914|gb|CD947150.1|CD947150
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|5361127|gb|AI795742.1|AI795742
EST:     CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
EST: gi|5762183|gb|AI967231.1|AI967231
EST:     CCCATCAAAGCTTGGCTATGGGCCTAAAGGCTCGCCACCTACTATTCCTG                         GTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC
genomic: CCCATCAAAGCTTGGCTATGGGCCTCAAGGCTCGCCACCTACTATTCCTGgtatgttttt ... cttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaggtgaacttctgcaggtcattgatgtgagccattttatctttcttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAACCAACCAACCAATCTGACGAGCTTTAGATTCATCAAACAAATGAATCCAT
                    cattgat  putative branch site (score: 4)
                                ccattttatctttctt  putative PPT
                                  attttatctttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggattcctgcaatgcctagcactgccacctgaatggattcctgcctaggtgaacttctgcaggtcattgatgtgagccattttatctttcttcttgcagGTGGAGCAACCCTCATATTTGACACGGAGCTTGTCGCTGTCAATGGAGAACCAACCAACCAATCTGACGAGCTTTAGATTCATCAAACAAATGAATCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT