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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagcctttataggcccatcgctttgcctttatctatatgtatgtctgtactgcctgttcttctcagctttcctaacatttgtttcctcgtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACATGGGGTTCCTCGACTTCTGCGAGAAGTGAAGAACCCATCAGACTGTCCA

Basic information

species Oryza sativa
transcript LOC_Os03g51650.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G149576_T01 (Zea mays), 3'ss of exon 11
-at-tagcctt-tataggcccatcgctttgcctttatctatatgtatgtctgtactgcctgttcttctcagctttcctaacatttgtttcctcgtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACATGGGGTTCCTCGACTTCTGCGAGAAGTGAAGAACCCATCAGACTGTCCA
 || |||| || |||  || | |    |||  ||  |||| ||  ||  ||    ||  | ||    ||     |  |  | | |  || |    |  ||||||||| ||||||||||||||||||||    ||||||||||| || || || |||||||||||| ||||||||||| |    | |  ||||||||||||| |
gatgtagcattatattagctcttttacttgt-ttcgtctaaatcaat--ctagtttgatttttaacttctctcctaatggcctcttgtttcggtgagtttcagGTGTCGTTGGAACCCAGAAGAGCATTTCGATGATCAACAATCACGAATATATGGGGTTCCTCAACTTCTGCGAGTAACTCAAACACCATCAGACTGTCGA
















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|86478929|gb|CI121562.1|CI121562
EST:     GATTGTCTTCATCCTATCCTCTGTCATCCTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|29669369|gb|CB665644.1|CB665644
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|66920616|gb|CX107464.1|CX107464
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|88243324|gb|CI244446.1|CI244446
EST:     TCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: TCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|87030251|gb|CI270261.1|CI270261
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|58598328|gb|CK008856.1|CK008856
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGC
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGC
EST: gi|4715480|gb|AU056597.1|AU056597
EST:     GATTGNCTTCATCCTATCCTCTGTCANCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|86502892|gb|CI145525.1|CI145525
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|86522037|gb|CI162243.1|CI162243
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|27577048|gb|CA999742.1|CA999742
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|702829|gb|D49120.1|D49120
EST:     CGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGNATCAGCATGATCAACAACCATGAGTACA
genomic: CGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|87021173|gb|CI271980.1|CI271980
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGAGCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|25803688|gb|CA759649.1|CA759649
EST:     GATTGTCTTCATCCTATCCTCTGTGATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|29633422|gb|CB638431.1|CB638431
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|29668996|gb|CB665271.1|CB665271
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|86499292|gb|CI141925.1|CI141925
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|27554258|gb|CA998158.1|CA998158
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|88965852|gb|CI006683.1|CI006683
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|29676184|gb|CB672459.1|CB672459
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|88251143|gb|CI349373.1|CI349373
EST:     TCTTCGCGATTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGATTACA
genomic: TCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|29625677|gb|CB630688.1|CB630688
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|86500204|gb|CI142837.1|CI142837
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|157650726|gb|EX450360.1|EX450360
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTAC
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTAC
EST: gi|29675120|gb|CB671395.1|CB671395
EST:     GATTGTTTTCATCGTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|396941381|gb|HO188590.1|HO188590
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
EST: gi|34475487|gb|CF452785.1|CF452785
EST:     GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGG                         GTGTTGTTGGAACC
genomic: GATTGTCTTCATCCTATCCTCTGTCATCTTCGCGAGTGCTCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACC
EST: gi|88850408|gb|CI093089.1|CI093089
EST:     TCTTACAATGG                         GTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA
genomic: TCTTACAATGGgtaatggcca ... gtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtactgcctgttcttctcagctttcctaacatttgtttcctcgtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACATGGGGTTCCTCGACTTCTGCGAGAAGTGAAGAACCCATCAGACTGTCCA
                          tcctaac  putative branch site (score: 1)
                                      tttcctcgt  putative PPT
                             taacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagcctttataggcccatcgctttgcctttatctatatgtatgtctgtactgcctgttcttctcagctttcctaacatttgtttcctcgtaaattcagGTGTTGTTGGAACCCAGAAGAGCATCAGCATGATCAACAACCATGAGTACATGGGGTTCCTCGACTTCTGCGAGAAGTGAAGAACCCATCAGACTGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - -tgccttt
- - - - - - - - - - - - - - - - - - - atgtatg
- - - - - - - - - - - - - - - - - - - - - - - -tgtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttc