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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcacaggtggctcggtgtagttagccgcaagctgtttatgttcagttctgaataccaatataaggcagaagttgtgagtgacacttccctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGATCTTTTTGAGCTCGGGGAAGACTCAGAGATCCAAG

Basic information

species Zea mays
transcript GRMZM2G008209_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008209_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g07880.1 (Oryza sativa), 3'ss of exon 4
tgtcacaggtggctcggtgtagttagccgcaagc--tgtttatgttcagttctgaatacca-atataaggcagaagttgtgagtgacact--tccctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGATCTTTTTGAGCTCGGGGAAGACTCAGAGATCCAAG
     || |  | |  || || ||  |         || ||   || |||||| ||| ||  || ||  | |  ||||||||||||||      ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||| | || ||||| || ||||| ||||| |||||||
-----caagctgttttgtttacttttctttcttttttgatttgttttagttctcaatgcctcatttagtggaagagttgtgagtgacatcagcgcctctttgcagTGGGAGCAAGCAACCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTTGATTTATTCGAGCTTGGTGAAGAATCAGATATCCAAG
















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|78120328|gb|DV538712.1|DV538712
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|211537799|gb|FL107888.1|FL107888
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|71437508|gb|DR818558.1|DR818558
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|71318841|gb|DR796181.1|DR796181
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|74243666|gb|DT651580.1|DT651580
EST:     GTATTTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATCCCTTTCTCGA
genomic: GTATTTT-CTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|91875001|gb|EB404958.1|EB404958
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|76014964|gb|DT942134.1|DT942134
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|89761605|gb|DY689549.1|DY689549
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|91871996|gb|EB401953.1|EB401953
EST:     GTATTTTCTTAAGGGCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGAT-CCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|71307844|gb|DR790143.1|DR790143
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|89757275|gb|DY686946.1|DY686946
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|148936771|gb|EC880907.2|EC880907
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
EST: gi|78118463|gb|DV536848.1|DV536848
EST:     GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCG                         TGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA
genomic: GTATTTTCTTAAGGCCGGCTACGCTGTCATCTTCATCCATCGCCGgtgagtcctt ... ctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctgaataccaatataaggcagaagttgtgagtgacacttccctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGATCTTTTTGAGCTCGGGGAAGACTCAGAGATCCAAG
                                      cacttccctctttgc  CT-rich tract
             aatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcacaggtggctcggtgtagttagccgcaagctgtttatgttcagttctgaataccaatataaggcagaagttgtgagtgacacttccctctttgcagTGGGAGCAAGCAGCCTTACTGTAGGTTTCTTCCAGAGGATTCCTTTCTCGATCTTTTTGAGCTCGGGGAAGACTCAGAGATCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC