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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttcttgtgcttcttactctatccatgcatatgcctttatctattttgttaaatctaatgaaatatgttttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCAGCATTTCAAGCAGCACTCCCAGACAGACAACCAGATGCCCCTTCCTCTA

Basic information

species Oryza sativa
transcript LOC_Os02g35590.2
intron # 8
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|88520540|gb|CI448194.1|CI448194
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88251938|gb|CI350366.1|CI350366
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88263359|gb|CI367133.1|CI367133
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88368430|gb|CI561504.1|CI561504
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGGGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88456348|gb|CI560951.1|CI560951
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|163927722|gb|EG712482.1|EG712482
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88503640|gb|CI431146.1|CI431146
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88512762|gb|CI440268.1|CI440268
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88521271|gb|CI448453.1|CI448453
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
EST: gi|88508803|gb|CI436309.1|CI436309
EST:     TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATG                         TTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA
genomic: TCCTCGCACCTCAGATTTATGCAGCAGTGACTCGTTTTCAAATTAACATGgtactgttct ... ttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatatgcctttatctattttgttaaatctaatgaaatatgttttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCAGCATTTCAAGCAGCACTCCCAGACAGACAACCAGATGCCCCTTCCTCTA
                            atctaat  putative branch site (score: 3)
                                         tgttttctt  putative PPT
           tttatctattttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgttcttgtgcttcttactctatccatgcatatgcctttatctattttgttaaatctaatgaaatatgttttcttggcagTTAAATTATCCCACTCTCGCGAGGCTCCATGAGGAGTATATGAAACATCCAGCATTTCAAGCAGCACTCCCAGACAGACAACCAGATGCCCCTTCCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG