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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGCCATATATGTATTCTTCTCCCGTAGAAAGAAGGATAATACTGTCATGCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggtttttctgttccatcatcatcttaccaatgcagaagttaagactatttcatggttaaatgaacttgtcagtttctgtagaaatttgttttctgca...

Basic information

species Oryza sativa
transcript LOC_Os12g01510.4
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01510.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G06670.1 (Glycine max), 5'ss of exon 5
ACTGCCATATATGTATTCTTCTCCCGTAGAAAGAAGGATAATACTGTCATGCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgt---tggtttt----tctgttccatcatcatcttaccaatgcagaagttaagact----atttcatggt-taaatgaacttgtcagtttctgtagaaatttgttttctgca--------------------------------------------------------------------
 | |||||   | |  | | || | | || || |||| |   ||||| |  || ||| | |||||||||||||| |||||  |||||||||||||| |||||   ||||  |    | |  |   |   |||| |    ||||  |  |  ||| |    | | ||   |  | || || |  | | |  ||  |  ||| | | |  |  |                                                                    
TCAGCCATTGCTTTTGTTTGCTTCAGAAGTAACAAGGTTGTAACTGTAAAACCTTGGACCACAGGGCTGAGTGGCCAGCTGCAGAAGGCATTTGTATCAGgtaattggtgctcatatttactttgtttacatcattggcatgctcagctatagatttcaaactgcaaaatgcatattaattattaactaactagaataatgtttatgttcaagtctttccatctttaacaagtggttctttgtttgaaattggcatactcatcgaacatgtatgatttag

upper sequence: LOC_Os12g01510.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G35570.1 (Glycine max), 5'ss of exon 5
ACTGCCATATATGTATTCTTCTCCCGTAGAAAGAAGGATAATACTGTCATGCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggtttttctgttccatcatcatcttaccaatgcagaagttaagactatttcatggttaaat-gaacttgtcagtttctgtagaaattt--gttttctgca-
 |   |||     |||   |||     | ||| ||||    |||||| |  || ||||| |||||  | |||||||||||  ||||||||||||||||||||   | |      |  |  |  |  | |  |  |||     | | | ||    || ||||| | | ||    |   | ||  || | | |     | |  || 
TCAATCATTGGCCTATATCTCTGTAAAACAAACAAGGTAGCTACTGTAAAACCTTGGGCAACAGGATTAAGTGGACAGCTTCAGAAGGCATTTGTAACAGgtaaatctcagcagtttaaaagtagttaagtagagcaatgactgaaaata----atagttaacttgcacacaactactgcttcaggattcttgaaatgcgacag
















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|58691771|gb|CK080458.1|CK080458
EST:     GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAG                         GTGTGCCTTCTCTTGAGAGGACAGAGCTGGAGGCGGCATGCGAGGGTTTTA
genomic: GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggttttt ... ttgtgtgcagGTGTGCCTTCTCTTGAGAGGACAGAACTGGAGGCGGCATGCGAGGGTTTCA
EST: gi|58609301|gb|CK037334.1|CK037334
EST:     GCCATGGACTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAG                         GTGTGCGTTCTCTTGAGAGGACAGAACTGGAGGCGGCATGCGAGGGTTTCA
genomic: GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggttttt ... ttgtgtgcagGTGTGCCTTCTCTTGAGAGGACAGAACTGGAGGCGGCATGCGAGGGTTTCA
EST: gi|29621673|gb|CB626684.1|CB626684
EST:     GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAG                         GTGTGCCTTCTCTTGAGAGGACAGAACTGGAGGCGGCATGCGAGGGTTTCA
genomic: GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggttttt ... ttgtgtgcagGTGTGCCTTCTCTTGAGAGGACAGAACTGGAGGCGGCATGCGAGGGTTTCA
EST: gi|29623656|gb|CB628667.1|CB628667
EST:     GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAAGCATTTGTAACAG                         GTGTGCCTTCTCT
genomic: GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggttttt ... ttgtgtgcagGTGTGCCTTCTCT
EST: gi|11442867|gb|BF430766.1|BF430766
EST:     GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAG                         GTGTGCCTTCTCTTGAGAGGACAGAACTGGAGGCGGCATGCGAGGGGTTCA
genomic: GCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggttttt ... ttgtgtgcagGTGTGCCTTCTCTTGAGAGGACAGAACTGGAGGCGGCATGCGAGGGTTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGCCATATATGTATTCTTCTCCCGTAGAAAGAAGGATAATACTGTCATGCCATGGGCTACAGGGCTGAGTGGACAGCTAAAGAAGGCATTTGTAACAGgttggtttttctgttccatcatcatcttaccaatgcagaagttaagactatttcatggttaaatgaacttgtcagtttctgtagaaatttgttttctgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG