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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttttcaaactataacctaaaactttttatatttaatttcctgtggattcactttgtcagactaaacttataacatactttttaccaatag

Basic information

species Oryza sativa
transcript LOC_Os01g44040.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44040.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 5'ss of exon 7
TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagt-cttttcaaactata-------acctaaaactttttatatttaatttcctgtggattcactttgtcagactaaacttataacatactttttaccaatag-----------------------------------------------
|||||||||   | |  |||||| |||||||||||||||||    |||||||||||| ||||||||||| || ||  | |||||       |  | || | ||| |    |||  ||      ||| |   | | |||   |   | |   ||| ||      |||||                                               
TGTTTATATTAGCTTGCGGAATTTCACTCAGCAGCTTAGAAGTTACTCTTTAACTCTCTTTGCgtaagttctctttgatctatatgatttaagttgaatcatttgactcataacctcacaaaaatttatagt-ttagaaacattgttttttatatttagagataatagttaacaactctgatttctctaactgtgccacacctttgtgcttctag
















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|86885457|gb|CI318608.1|CI318608
EST:     CTAAGG-A-TGCACTCAGCAGCGTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|87006678|gb|CI285712.1|CI285712
EST:     CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|88995453|gb|CI022776.1|CI022776
EST:     AGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: AGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|88477010|gb|CI414281.1|CI414281
EST:     GGAATTGCACTCAGCAGCTTAGAAACTTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: GGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|29659100|gb|CB655375.1|CB655375
EST:     CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|88846659|gb|CI373427.1|CI373427
EST:     GTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: GTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|88515591|gb|CI443245.1|CI443245
EST:     CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTGTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|86498852|gb|CI141485.1|CI141485
EST:     CGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|89177189|gb|CI043692.1|CI043692
EST:     CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|86502826|gb|CI145459.1|CI145459
EST:     CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|88956170|gb|CI092458.1|CI092458
EST:     CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: CTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
EST: gi|88507120|gb|CI434626.1|CI434626
EST:     TAGAAACGTCTCTTTAACTCTTTTTGC                         GTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG
genomic: TAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttt ... ttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTATATCTCCCTAAGGAATTGCACTCAGCAGCTTAGAAACGTCTCTTTAACTCTTTTTGCgtaagtcttttcaaactataacctaaaactttttatatttaatttcctgtggattcactttgtcagactaaacttataacatactttttaccaatag

- - - - - - -  AAGGAA
- - - - - - - - - - - - - - - GCAGCT