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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGCAGTGGAGCGAGAAGAGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttcatttcgcagcaactttgtttctactatttttgattcattgagcctatatttcttcctgtccagagcttcgatcgacccaatataaatgcga...

Basic information

species Oryza sativa
transcript LOC_Os01g68380.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68380.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G401050_T01 (Zea mays), 5'ss of exon 11
TTGGCAGTGGAGCGAGAAGAGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttcatttcgcagca--actttgtttcta------------ctatttt-tgattcattgagcctatatttct-tcctgtccagagcttcgatcgaccc---aatataaatgcga----------------------------------------------------------------------------
|| ||||||||| |||||||  ||||||||||  |||||||||| |||||||| ||||||||||||||||| |||    | ||  ||    ||   |  ||||            || |||  |||   | | |  | ||  |||| |  | || |  ||||| ||| |      ||| |   |||                                                                              
TTAGCAGTGGAGAGAGAAGAACTGCTGCGAGCACTGAGAATTGAGTCATCCAACTGCTCCAAGCTGAAGgtattggctctctcttagtctcacgcagcatctagaggtcagatgcctgtttcatgacatagttaagccatggttctgttttatcaaatgcttctatctattggaaaatttgtttgcagttcaacacgtcaagcaagccttgtgttacttctgtaattgtacatctactaatgctatttactttgtatcctgtag

upper sequence: LOC_Os01g68380.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G166873_T01 (Zea mays), 5'ss of exon 11
TTGGCAGTGGAGCGAGAAGAGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttcatttcgcagcaacttt--gtttctactatttttgattcattgagcctatatttcttcctgtccagagcttcgat-cgacccaatataaatgcga
|| | ||||||| |||||| | ||||||||||  |||||||||| |||||||| ||||||||||||||||| |||   || ||  |    | |   |  || | || | | | |    ||  | ||| |     | |    |   | | | | |      ||  |  | |  
TTAGTAGTGGAGAGAGAAGCGCTGCTGCGAGCACTGAGAATTGAGTCATCCAACTGCTCCAAGCTGAAGgtattgactatctcttactctcatgcagcatcgagtaatgtaggtgagatg--cttatttcatgacatagtgaagccctgggttctgttttatggagcttct-
















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|14713542|gb|AU197540.1|AU197540
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|86478032|gb|CI120665.1|CI120665
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGGCTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|86596871|gb|CI270667.1|CI270667
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|58674576|gb|CK063263.1|CK063263
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCCATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCCAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|29670331|gb|CB666606.1|CB666606
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|87014864|gb|CI271463.1|CI271463
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|29672335|gb|CB668610.1|CB668610
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|58682563|gb|CK071250.1|CK071250
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|66924680|gb|CX111528.1|CX111528
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATC
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATC
EST: gi|29644364|gb|CB649371.1|CB649371
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
EST: gi|29668123|gb|CB664398.1|CB664398
EST:     AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAG                         GAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT
genomic: AGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttca ... tgtcttaaagGAATTGAACAAGGATCTAACGCAAAAGCTGGAGATTCAGACTCACAGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGCAGTGGAGCGAGAAGAGTTGCTGCGAGCTTTGAGAATTGAATCATCCAATTGCTCCAAGCTGAAGgttttgttcatttcgcagcaactttgtttctactatttttgattcattgagcctatatttcttcctgtccagagcttcgatcgacccaatataaatgcga

- - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG