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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctatccttttgttttcttgagtgtttattttatagtgtttcctcatggtatgtttctctactgagattatagatatctaaccatttattatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTTGCACCAGCAACTAC

Basic information

species Oryza sativa
transcript LOC_Os09g24200.1
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|88410051|gb|CI573290.1|CI573290
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|58672603|gb|CK061289.1|CK061289
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|88400724|gb|CI596145.1|CI596145
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|33691318|gb|CF319557.1|CF319557
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCANATCAG                         GCTCCCNCTACTCANACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|56157493|gb|D24336.3|D24336
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACT-CAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGT
EST: gi|88317010|gb|CI625647.1|CI625647
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCGTGCAGCTCCTGCATCTCAAGCACCAGT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCC-TGCAGCTCCTGCATCTCAAGCACCAGT
EST: gi|88316529|gb|CI622775.1|CI622775
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|58686007|gb|CK074694.1|CK074694
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|88377574|gb|CI605409.1|CI605409
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|88717896|gb|CI739408.1|CI739408
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCT
EST: gi|58602384|gb|CK012912.1|CK012912
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCT
EST: gi|58665783|gb|CK054469.1|CK054469
EST:     GGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: GGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|86884299|gb|CI311704.1|CI311704
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|88693324|gb|CI736899.1|CI736899
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACA
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACA
EST: gi|29678389|gb|CB674664.1|CB674664
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|88399554|gb|CI583288.1|CI583288
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|88346546|gb|CI623003.1|CI623003
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTAATCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCA
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCA
EST: gi|88405923|gb|CI591318.1|CI591318
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|58609238|gb|CK037271.1|CK037271
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
EST: gi|88571905|gb|CI663278.1|CI663278
EST:     AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG                         GCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT
genomic: AGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAGgtgagatgga ... tatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggtatgtttctctactgagattatagatatctaaccatttattatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTTGCACCAGCAACTAC
                               atctaac  putative branch site (score: 2)
                      attatagatatctaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctatccttttgttttcttgagtgtttattttatagtgtttcctcatggtatgtttctctactgagattatagatatctaaccatttattatttgccagGCTCCCCCTACTCAAACAGTGCCTGCAGCTCCTGCATCTCAAGCACCAGTTGCACCAGCAACTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC