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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaattctgtaacacttgtttgcaggaatgttaggacagcttattgtcagttatcttagggagaaagctaatggtggtaattcttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAATCCTCCTCCTGAAAAGGACTATGAAGTATATTTCAAAGAACTCAAAGAAG

Basic information

species Zea mays
transcript GRMZM2G019358_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 15
--------------gttgaattctgtaacacttgtttg--caggaatgttaggacagcttattgtca-gttatcttagggagaaagctaatggtggtaattcttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAATCCTCCTCCTGAAAAGGACTATGAAGTATATTTCAAAGAACTCAAAGAAG
                | | ||     |||||  || |  ||  ||   |     ||   |||||    || | ||       |||||||     ||| || || |  | ||||||||||||||||||||||||| ||||| |  ||| |||| ||| ||||||||||||| || || |||||||| || ||||||||||| |||||||  |
gttaaaattctgcaactcatttgcaagacactacttgggacaacaaaacttcagaaggaaattgtggcattttatttcattttaagctaactcatgtacttttttttgttagGTCAAGAGCACTGTTCCATTCAGTGAACCTTTCGTGGTTGATCCTTCAAATCCTCCTCCAGAGAAAGACTATGATGTGTATTTCAAAGAGCTCAAAGCTG

upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 15
-gttgaattctgtaacacttgtttgcaggaatgttaggacagcttattgtcagttatcttagggagaaagctaatggtggtaattct----tatgat-cagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAATCCTCCTCCTGAAAAGGACTATGAAGTATATTTCAAAGAACTCAAAGAAG
  |||  |         | ||  |  || ||| | |   | | | | | ||| |    || |  ||  |||||       | |||||    | || | |||||||| ||     ||||||| || || || |      | || || ||||| |||||||| |||||||||||||| |||||||| ||| |  | |||||||
aattgtttatccgtgttcatggatctagtaatttgattgcggat-agtctcattctattttgcaagctagctacacaatctcattctaatatgtgttgcagGTCAAAAGTGTCATTCCATTTAGTGAGCCATTCACTGTGGATCCAGCAAACCCTCCTCCAGAAAAGGACTATGACGTATATTTTAAAAATTTAAAAGAAG

upper sequence: GRMZM2G019358_T03 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G12480.1 (Glycine max), 3'ss of exon 15
----gttgaattctgtaacacttgtttgcaggaatgttaggacagcttattgtcagtt--atcttagggagaaagcta-atggtgg-taattcttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAATCCTCCTCCTGAAAAGGACTATGAAGTATATTTCAAAGAACTCAAAGAAG
    | | |||| | || | | || |    |   |  ||     | || | |  |||   ||  ||    | |||||| ||  |   ||||   |||   |||||||| ||     ||||||| ||||| || | |    | || ||  |||| |||||||| |||||||||||||| |||||||| ||| |  | |||||||
ttgagataaattgtttatc-cgtgctcatggatctagtaattt-gattgtggatagtctcattctatttggcaagctacataatctctaatatgtattg-cagGTCAAAAGTGTCATTCCATTTAGCGAGCCATTTACTGTGGATCCAACAAACCCTCCTCCAGAAAAGGACTATGACGTATATTTTAAAAATTTAAAAGAAG

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|211050961|gb|FL383301.1|FL383301
EST:     CCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: CCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|78022714|gb|DV491101.1|DV491101
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|10450883|gb|BE924807.1|BE924807
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAACCTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|211357416|gb|FL471654.1|FL471654
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|7304470|gb|AW600409.1|AW600409
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|211023893|gb|FL457612.1|FL457612
EST:     TCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|4730655|gb|AI649821.1|AI649821
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|13562283|gb|BG550503.1|BG550503
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|12968100|gb|BG265047.1|BG265047
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|32934374|gb|CF039186.1|CF039186
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGGGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
EST: gi|7216720|gb|AW562842.1|AW562842
EST:     TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAG                         GTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT
genomic: TTTGTGTAGCAGCTCTGGCAAGCCCAGATGCTGTGGGCAAAACTTTCGAGgttgaattct ... ttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttattgtcagttatcttagggagaaagctaatggtggtaattcttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAATCCTCCTCCTGAAAAGGACTATGAAGTATATTTCAAAGAACTCAAAGAAG
                           agctaat  putative branch site (score: 3)
                                          ttcttat  putative PPT
                                       taattcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaattctgtaacacttgtttgcaggaatgttaggacagcttattgtcagttatcttagggagaaagctaatggtggtaattcttatgatcagGTCAAGAGCACTGTTCCATTCAGCGAACCGTATGTGATTGACCCTGCAAATCCTCCTCCTGAAAAGGACTATGAAGTATATTTCAAAGAACTCAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG