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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCGATGGACAGGCATCTGTTGAGGCTCAAGAGTTTGGATTGGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatccattcttcttgtggattcattcaattcatctaggactccagattgagcatctggcaatgactccacccagtgttgtattaccaaaaccgtc...

Basic information

species Zea mays
transcript GRMZM2G006468_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006468_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g26870.3 (Oryza sativa), 5'ss of exon 9
ACCCGATGGACAGGCATCTGTTGAGGCTCAAGAGTTTGGATTGGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatccattcttcttgtggattcattca-attcatcta-ggactccagattgagcatctggcaatgactc--cacccagtgttgtattaccaaaaccgtc
||| ||||| ||| ||| ||| ||||||||||||||||||||| |   |||||||||||||||||| || |||||||||||||| ||||||||||||  |    || | ||||||  | ||| | ||||||| | | ||      ||     |  ||  | || ||  ||     |  ||| | || |  ||    
ACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAACATGCTCATTGCAGCTGTTGAAGAGAGATACAAAGATGCTGgtaattttattatcgtgttgtggtgttattaagattcatcgatgcacctttttttttttttgcggggaagattcatcagtgcattctgtctgacaaggac----
















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|60396153|gb|DN229022.1|DN229022
EST:     GGTGAAG-ACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|37426214|gb|CF650858.1|CF650858
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|33100890|gb|CF060850.1|CF060850
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGTGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|14244855|gb|BG842793.2|BG842793
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|16925921|gb|BM078989.1|BM078989
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|76010925|gb|DT938095.1|DT938095
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|14243138|gb|BG840841.2|BG840841
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|116813437|gb|EC855888.1|EC855888
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|60353604|gb|DN220577.1|DN220577
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|211186706|gb|FL252851.1|FL252851
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAAACTGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAA-CTGG
EST: gi|71774336|gb|DR972214.1|DR972214
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|60346391|gb|DN213364.1|DN213364
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTTTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|89755425|gb|DY685846.1|DY685846
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTTTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|33100633|gb|CF060593.1|CF060593
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|18650378|gb|BM499197.1|BM499197
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAGCTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|211436290|gb|FL481825.1|FL481825
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|28984501|gb|BQ539125.2|BQ539125
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|60358728|gb|DN225701.1|DN225701
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|60353656|gb|DN220629.1|DN220629
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAAATGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|33102029|gb|CF061989.1|CF061989
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|13178561|gb|BG349819.1|BG349819
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|13177701|gb|BG349130.1|BG349130
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|13177698|gb|BG349129.1|BG349129
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|211507463|gb|FL431647.1|FL431647
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|211505179|gb|FL436188.1|FL436188
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
EST: gi|16377885|gb|BI992166.1|BI992166
EST:     GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG                         CATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG
genomic: GGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatcc ... gcttcgacagCATCATGGAAGGACAAACTGATGCGGCTGAGGTCTAAGCGGAAGAACTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCCGATGGACAGGCATCTGTTGAGGCTCAAGAGTTTGGATTGGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTGgtaatgatccattcttcttgtggattcattcaattcatctaggactccagattgagcatctggcaatgactccacccagtgttgtattaccaaaaccgtc

- - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG