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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG

Basic information

species Zea mays
transcript GRMZM5G868168_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g46740.1 (Oryza sativa), 3'ss of exon 3
gcattctgttcactgttatatt-ttgatgttttcatgactcagtaggtttggtttgttgtagt-tatgattcaaa-ataatgtta--tacttttgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
     ||    |   |||  |  |||||  ||| || |     | | ||   ||  || |||  |    ||||   ||  |   |  || | || ||||||||||||| || ||||| ||||| |||||||| ||||| || || ||||| |||||| | |||||||||||||||||||| || ||||| ||||||
agtcactaggaatcattacttagttgattattttataatcttttggtttcatttatttttagcctgcagttcagttatggttcaaattattattatgtagATTAGACACGGAGAAGCCGTTGGAATAATTGGTCCTTCGGGAACAGGAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG

upper sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
--gcat-tctgttcactgtta-tattttgatgttttcatgactcagtaggt-ttggtttgttgtagttatgattcaaaataatgttatacttt-tgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
    || |    |   ||| | |     || || ||   || |||| |  |  |   |  || |  |  |  |||    |  | ||  || |  ||  ||||| |  ||||||||||| ||||| |||||||| || || ||||| || ||||| ||  | |||||| |||| || || || |||||||||||||| 
ttaaatgtaaactagttgtaagtggggggaggtcttgcagattcagaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-

upper sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
gcattctgttcactgttatattttgat--gttttcatgactcagtag--gtttggt-ttgttgtagttatgattcaaaataatgttatacttttgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
 |||| | || |    |  |||| |    || ||  ||| |||| |   |||   | || |||  ||| |  ||     |  |  |    |  ||  |||||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||| ||  | |||||| |||| ||||| || |||||||||||||| 
ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA

upper sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
-----gcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttat--acttttg----tgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
        || |||| || || ||      | | ||  |    |    |||        |           |  ||  | | | | |   | ||||     || ||||||||||||||||||| |||||| | ||||| ||||| || || ||||||||||| || || ||| |||||||||| || |||||||| ||||||
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG

upper sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 2
-------gcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttata-cttttgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
          || |||      ||  || || |  ||  | ||| |   | | | || ||| |  |  |     || |   |  |  | || |   | | |||||||||||||| ||||| |||||||| ||||| ||||| || || || ||||||||  |  ||||| |||| || || || |||||||| ||||||
gagtggatttttttgtctctcttttcatatttagtttcccttgaattt-tggttatgttttatcat--tctctgtttattttcttactttaacccatttatagATTAGACATGGGGAAGCTGTTGGGATTATTGGGCCTTCTGGCACTGGGAAATCAACAGTTCTGAAGATTATTGCGGGACTTCTTGCTCCAGACAAG

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|50324151|gb|CO519277.1|CO519277
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|31350150|gb|CD434507.1|CD434507
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|154130463|gb|EC872173.2|EC872173
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|148986921|gb|EE030732.2|EE030732
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|78103984|gb|DV522402.1|DV522402
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAAC
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAAC
EST: gi|76931706|gb|DV172823.1|DV172823
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|149004790|gb|EE039293.2|EE039293
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|91048130|gb|EB158548.1|EB158548
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|149078033|gb|EE166771.2|EE166771
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|78120174|gb|DV538558.1|DV538558
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGATTAG                     
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTC---A--AGgtcagctttt ... tgtaga
EST: gi|149080766|gb|EE169831.2|EE169831
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAAC
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAAC
EST: gi|33467141|gb|CF244190.1|CF244190
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|19057652|gb|BM736319.1|BM736319
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGATTAG                     
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTC---A--AGgtcagctttt ... tgtaga
EST: gi|211065956|gb|FK946601.1|FK946601
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagA-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|211380394|gb|FK976874.1|FK976874
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ACATGGTGAAGCAGTTGGGA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... tgtagattagACATGGTGAAGCAGTTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
                                       cttttgt  CT-rich tract
                ttatgattcaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT