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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtcagaatctgaacatatgtagatgtgttgatgcgcaacatatcctaaactttatactcttttttatatgttatcaatatgtaacaatttttccacagGACTTGGGTTATCCATCCTCTGCAAAAACTGAACAGTTAGTGACTTCATCAGTTAAAGGAGTATCAAGCGGCAGTAAAGGAAATGAAGCAGTCAACACGA

Basic information

species Oryza sativa
transcript LOC_Os01g49310.2
intron # 3
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|29622013|gb|CB627024.1|CB627024
EST:     GATTTGCTTCAGCATCAATGCAAAAG                         GACTTGGGTTATCCATTCTCTGCAAAAACTGAACAGTTAGTGACTTCATCA
genomic: GATTTGCTTCAGCATCAATGCAAAAGgtattagcac ... ttttccacagGACTTGGGTTATCCATCCTCTGCAAAAACTGAACAGTTAGTGACTTCATCA
EST: gi|218487953|gb|FG943628.1|FG943628
EST:     GATTTGCTTCAGGGATCAATGCAAAAG                         GACTTGGGTTATCCATTCTCTGCAAAAACTGAACAGTTAGTGACTTCATCA
genomic: GATTTGCTTCA-GCATCAATGCAAAAGgtattagcac ... ttttccacagGACTTGGGTTATCCATCCTCTGCAAAAACTGAACAGTTAGTGACTTCATCA
EST: gi|86891181|gb|CI305955.1|CI305955
EST:     GATTTGCTTCAGCATCAATGCAAAAG                         GACTTGGGTTATCCATCCTCTGCAAAAACTGAACAGTTAGTGACTTCATCA
genomic: GATTTGCTTCAGCATCAATGCAAAAGgtattagcac ... ttttccacagGACTTGGGTTATCCATCCTCTGCAAAAACTGAACAGTTAGTGACTTCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaaactttatactcttttttatatgttatcaatatgtaacaatttttccacagGACTTGGGTTATCCATCCTCTGCAAAAACTGAACAGTTAGTGACTTCATCAGTTAAAGGAGTATCAAGCGGCAGTAAAGGAAATGAAGCAGTCAACACGA
                                            tttttccac  CT-rich tract
              tcttttttatatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtcagaatctgaacatatgtagatgtgttgatgcgcaacatatcctaaactttatactcttttttatatgttatcaatatgtaacaatttttccacagGACTTGGGTTATCCATCCTCTGCAAAAACTGAACAGTTAGTGACTTCATCAGTTAAAGGAGTATCAAGCGGCAGTAAAGGAAATGAAGCAGTCAACACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC