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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattcctaacttccctatgatgtcaatacaattaaaatcgccattttacactaacatactatatcctgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 15
gttattcctaacttccctatgatgtcaatacaattaaaatcgccattttaca--ctaacatactatatcctg-----tactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG
  ||| | ||| |   ||  | |   ||      |    |  | || |   |  ||   |||  | |  |||     |  | ||||| |||||||| |||||||||||||| |||| |||||||||  | || || ||||| ||  | || ||||| ||||| || |||||||| ||||||||||
-gtatgcttaaatattct-cggttcaaacttgtcttggtttactatctagaaatcttgtatataaaacgctgctttttgttttagGCACTGGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 14
gttattcctaacttccctatgatgtca-atacaattaaaatcgccattttacactaacat--actatatcctgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG
                       || | | ||| ||| |       |  |  |  | |||  | | | || | |  || ||||  ||||    ||||||||| | | |||||   | || |||   ||  |||||||||| ||||||||| |||| ||||| ||||||||||| || ||||
-----------------------gtgagagacatttatatcttgtctcgtggaaaaccattgattgtttcttttgatgcagGCATTGGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTG

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 15
gttattcctaacttccctatgatgtca-atacaattaaaatcgccattttacactaacat--actatatcctgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG
                       || | | ||| ||| |       |  |  |  | |||  | | | || | |  || ||||  ||||    ||||||||  | | |||||   | || |||   ||  |||||||||| ||||||||| |||| ||||| ||||||||||| || ||||
-----------------------gtgagagacatttatatcttgtctcgtggaaaaccattgattgtttcttttgatgcagGCATTGGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTG

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|58611693|gb|CK039405.1|CK039405
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGAGAAGTTTGATCCAGATTTCCTTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
EST: gi|33804193|gb|CF327971.1|CF327971
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
EST: gi|88735905|gb|CI757480.1|CI757480
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
EST: gi|66919084|gb|CX105932.1|CX105932
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA
EST: gi|29617005|gb|CB622017.1|CB622017
EST:     AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAG                         GCTCTGGAATCCTTCTATGACAAGTTTGATCGAGATTTCATTGATATTAGA
genomic: AGCATTTCCCATCTGTCAATTGGCTCATCTCTTACTCAAAATACTCAAAGgttattccta ... tgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaatacaattaaaatcgccattttacactaacatactatatcctgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG
                           cactaac  putative branch site (score: 1)
     tacaattaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattcctaacttccctatgatgtcaatacaattaaaatcgccattttacactaacatactatatcctgtactgtagGCTCTGGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA