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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctatttttcaagtttgtaataattaaaactcaattaattatacgctaataccaccccgttatacgtaataaacataatcttcatcttaatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCATGCAGATGCAGATTGTTGGGTTGATGTTCGACGTCTCTGATTTGACCTTC

Basic information

species Oryza sativa
transcript LOC_Os06g26234.1
intron # 21
splice site 3'
intron type U2

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|88485603|gb|CI422874.1|CI422874
EST:     AATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: AATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|89193939|gb|CI018257.1|CI018257
EST:     TT-A-ATCTGAACTCTTGCAAACTTACAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88380936|gb|CI523507.1|CI523507
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88905996|gb|CI089582.1|CI089582
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88474382|gb|CI411653.1|CI411653
EST:     GAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: GAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88478055|gb|CI415326.1|CI415326
EST:     AACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: AACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|86872605|gb|CI325229.1|CI325229
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88282952|gb|CI404200.1|CI404200
EST:     AATATGTGAACTCTTGCAAACTTNAAGATTCGCATGGCAAAAACTGAGG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCA
genomic: AATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGA-Ggtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCA
EST: gi|86868828|gb|CI334200.1|CI334200
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|58681802|gb|CK070489.1|CK070489
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAG-G-ATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88438943|gb|CI531123.1|CI531123
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|29639222|gb|CB644231.1|CB644231
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|29639178|gb|CB644187.1|CB644187
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88472480|gb|CI409751.1|CI409751
EST:     TAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TAATATCTGAACTCTTGCAAACTTAAAGATTCGCAT-GGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
EST: gi|88274273|gb|CI394679.1|CI394679
EST:     TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAG                         GGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT
genomic: TTAATATCTGAACTCTTGCAAACTTAAAGATTCGCATGGCAAAAACTGAGgtaatgggta ... taatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgctaataccaccccgttatacgtaataaacataatcttcatcttaatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCATGCAGATGCAGATTGTTGGGTTGATGTTCGACGTCTCTGATTTGACCTTC
                                          tcttaat  putative branch site (score: 3)
                                    tcttcatctt  CT-rich tract
                        taataaacataatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctatttttcaagtttgtaataattaaaactcaattaattatacgctaataccaccccgttatacgtaataaacataatcttcatcttaatcttcagGGGAAAAGAACACCACCGTAGTGAGAGGATCCTTCAGGTATGAATGTCCATGCAGATGCAGATTGTTGGGTTGATGTTCGACGTCTCTGATTTGACCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT