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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgggaagcaagaagagcactccataaactatgtgtttttgcatgcacatatacatttcaaacgcaaagtatagttcatattctgcttggcatgttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACGCCTCTGCCTGACAGTCCCGGATCTGTGGAGGGCTCTTTCACGTTTGTTC

Basic information

species Oryza sativa
transcript LOC_Os11g16390.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g16390.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G06110.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgcgggaagcaagaagagcactccataaactatgtgtttttgcatgcacatatacatttcaaacgcaaagtatagttcatattctgcttggcatgttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACGCCTCTGCCTGACAGTCCCGGATCTGTGGAGGGCTCTTTCACGTTTGTTC
|| |  |    ||    ||  ||    |  ||| || ||||| |  | | ||  | |    |    ||     | |  |    | |||| || |  |  | | || ||||||| ||  ||    | ||  |||||||||||||||||||||||||  |   | | ||    | | | |||||  | || ||||||||||| ||||| |
gtgta-gttttgcttttagttcaagataacaacaatttgtttgttgaaggaccaacagtcgttttccgttt--tgtgatatgaactctgttttg--ttatatttgtagTACCCGCTCTTACAAGCCGGGGAGGAAGAGTTTGTGTATGAGAGTTGTTCCAGTTTTCCGACAACTGCTGGATCCATTGATGGCTCTTTCACCTTTGTAC
















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|29664981|gb|CB661256.1|CB661256
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|29664982|gb|CB661257.1|CB661257
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|8858290|gb|AU095608.1|AU095608
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|29664979|gb|CB661254.1|CB661254
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|29677579|gb|CB673854.1|CB673854
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|29658842|gb|CB655117.1|CB655117
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|29645119|gb|CB650126.1|CB650126
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|13420665|gb|AU174755.1|AU174755
EST:     GGAGAGACCGGGTTGTTTNTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|29664980|gb|CB661255.1|CB661255
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
EST: gi|5038982|gb|AU071092.1|AU071092
EST:     GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAG                         TACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG
genomic: GGAGAGACCGGGTTGTTTCTGATGTGAACGGGGAAGGTGTTATTGGGAAGgtatgcggga ... ttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacatttcaaacgcaaagtatagttcatattctgcttggcatgttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACGCCTCTGCCTGACAGTCCCGGATCTGTGGAGGGCTCTTTCACGTTTGTTC
     atttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgggaagcaagaagagcactccataaactatgtgtttttgcatgcacatatacatttcaaacgcaaagtatagttcatattctgcttggcatgttctgtgcagTACCCTCTACTAACTACAGGCCAGGAAGAGTTTGTGTATGAGAGTTGCACGCCTCTGCCTGACAGTCCCGGATCTGTGGAGGGCTCTTTCACGTTTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG