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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGAAGATGGTTCATTGGATGAAAATGTTGAATCTTTTCTATCTCAGGATGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaatatcctgctgatacctggctgctgtatgcaatcaacaggagtcataaataaatgaacatagtctcactaataatctgcattttttatcttg...

Basic information

species Oryza sativa
transcript LOC_Os01g42260.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G425377_T01 (Zea mays), 5'ss of exon 4
CTAGAAGATGGTTCATTGGATGAAAATGTTGAATCTTTTCTATCTCAGGATGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtat--tttaatatcctgctgatacctggctgctgtatgcaatcaacaggagtcataaataaatgaacatagtctcactaataatctgcattttttatct-tg--------
||||||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||||||||    |||||||| | |||||||||||||||||||||  |||  | ||||  |||||| ||| |      ||   | |||     |  |   |    || |||  | | |   || |  |  || |||||| | ||        
CTAGAAGATGGCTCATTGGATGATAATGTTGAATCTTTTCTATCACAGGATGACATGGATCCTAGGGACAACTTGGGGCGATGCATGGATGCTAGTAAAGgtatggttttgtttccttgtgatacatggtt------tgattttaac-----ttgtccttgtgagagcatgtttttatccatgacatagatattttatttatggcttgctg

upper sequence: LOC_Os01g42260.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G022383_T02 (Zea mays), 5'ss of exon 9
CTAGAAGATGGTTCATTGGATGAAAATGTTGAATCTTTTCTATCTCAGGATGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaatatcctgctgatacctggct--gctgtatgcaatcaacaggagtcataaataaatgaacatagtctcactaataatctgcattttttatcttg
|| |||||||| ||||||||||| |||||||||||||||||||| |||||||||||||| ||||||||    |||||||| | |||||||||||| |||||| |  |  | |    ||  ||||||  |    | |      ||     ||||   |  |   |   |||    |  ||||||       | ||||||    
CTGGAAGATGGCTCATTGGATGATAATGTTGAATCTTTTCTATCACAGGATGACATGGATCCTAGGGACAACTTGGGGCGATGCATGGATGCTAGCAAAGgtgtggttttgtttc-cttgtacctgttttgattttgacttgtccttgtgagt-gcacgtttttatccatgacatagctaatagctattttgttttatgcct
















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|58671957|gb|CK060643.1|CK060643
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTAGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|58655398|gb|CK044078.1|CK044078
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|33794564|gb|CF323169.1|CF323169
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGGTTTTGGTTNTTGCTGAAGTNTGCGAAGGCACCGTGCAAGTGCAACCAA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGG-TTT-GGTT-TTGCTGAAGT-TGCGAAGGCAC-GTGCAAGTGCAACCAA
EST: gi|58665681|gb|CK054367.1|CK054367
EST:     TGACCTGGACCCTA-GGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|58608277|gb|CK036310.1|CK036310
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GG-TTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|33794705|gb|CF323235.1|CF323235
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTT
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGG-TTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTT
EST: gi|66923385|gb|CX110233.1|CX110233
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|58604540|gb|CK015068.1|CK015068
EST:     ATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: ATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|32948512|gb|BP185084.1|BP185084
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|58598175|gb|CK008703.1|CK008703
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|33797972|gb|CF324846.1|CF324846
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTA
EST: gi|58591655|gb|CF989963.1|CF989963
EST:     TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAG                         GGTTCGGTTTTGCTGAAGTTGCGAAGGCACG
genomic: TGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaat ... gtttatacagGGTTTGGTTTTGCTGAAGTTGCGAAGGCACG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAGAAGATGGTTCATTGGATGAAAATGTTGAATCTTTTCTATCTCAGGATGACATGGACCCTAGGGATTCATTGGGGCGCTCCATGGATGCTAGTAAAGgtattttaatatcctgctgatacctggctgctgtatgcaatcaacaggagtcataaataaatgaacatagtctcactaataatctgcattttttatcttg

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
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