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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacatattttctgaagctggagcaaataatcaatttcaataatttgtgttgcatctgtgactgtccatgtaactgactttgttgatattgctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCCCCAACACCAAGGAAACCTCAGAATCTGTAGGGGTGCAGACTGCACAAGC

Basic information

species Oryza sativa
transcript LOC_Os11g43590.4
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G18590.1 (Arabidopsis thaliana), 3'ss of exon 16
aaacatattttctgaagctggagcaaataatcaatttcaataatttgtgttgcatctgtgactgtccatgtaactgactttgttgata--ttgctttgc---cagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCCCCAACACCAAGGAAACCTCAGAATCTGTAGGGGTGCAGACTGCACA-AGC-
                    | |  | | || |   ||||||   | | ||  |  |   | | || |  |     | | |  | | |  |||   ||    |||||||||||||| ||||||||||||||  | ||| |  | ||    ||| |  | ||||| || || |||    || | ||      |||||   | | | | 
--------------------gtgtca-tcataatcatcaatagactctattcaaatttgcattttcaaaatgtagtattgttctaaaaacttgagatgaacgcagGTTGAAGTGTTTCATCTGAAGCAAAGATTACAATCTCTAGAGAACAGAGCTGCTACACCCAGAAAGCCTTTCCATGTCTAAA--CACAGACCAGAGACAACA
















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|88459518|gb|CI519579.1|CI519579
EST:     CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAG                         GTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC
genomic: CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAGgtaaatggtg ... gctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC
EST: gi|88275715|gb|CI396319.1|CI396319
EST:     CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAG                         GTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC
genomic: CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAGgtaaatggtg ... gctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC
EST: gi|88381956|gb|CI530762.1|CI530762
EST:     CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAG                         GTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC
genomic: CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAGgtaaatggtg ... gctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC
EST: gi|88321370|gb|CI535322.1|CI535322
EST:     CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAGG                         GTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATC
genomic: CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCA-Ggtaaatggtg ... gctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATC
EST: gi|88320493|gb|CI523236.1|CI523236
EST:     CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAG                         GTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC
genomic: CTACTCGCGGAGTTTTAGCAGGAGAACGCTCGAGGGCCTTCCAGCTCCAGgtaaatggtg ... gctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttgcatctgtgactgtccatgtaactgactttgttgatattgctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCCCCAACACCAAGGAAACCTCAGAATCTGTAGGGGTGCAGACTGCACAAGC
                                           ttgcttt  CT-rich tract
                                     ttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacatattttctgaagctggagcaaataatcaatttcaataatttgtgttgcatctgtgactgtccatgtaactgactttgttgatattgctttgccagGTTGAAGTGTTCCATCTGAAGCAAAGGCTGCAAACAATGGAAGGAAGATCCCCAACACCAAGGAAACCTCAGAATCTGTAGGGGTGCAGACTGCACAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA