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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactctaatttgcatgcttttctgtttggaaggaagtggcattgattcttgaaaccaagtgtgacatatatatatacatgttgtgatatatttgtatgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g01014.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01014.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G005859_T02 (Zea mays), 3'ss of exon 6
-------------------------------------------------gtgactctaatttgcatgcttttctgtttggaagg-------aagtggcattgattcttgaaaccaagtgtgaca-tatatatatac----atgttgtgatatatttgtatgattg-cagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG
                                                 || | | |  ||||  |  |||  | | |  | |        | || |  || || ||||||| | | |   ||  ||||||| |      |   || | | |      |  |||  |||| ||||| ||||||||||||||||| ||||||||    || ||||| ||||| |||||||||||||||||||
gtgacccagatgtcctcctgacgacgacagtcctgattcgcgtgactatgttaatttcttttgttttttttcttatctccaggctccagctaggtagtgttaat-cttgaaatctattaaaaccctatatatgtgaggtgacaatgcgctgttcactcaaaattttcagACCCTACGTATGTGGTGACACCAGCGATGCGTTCGCGCACAGGGCGTGAGAACCTCAAGAAACTATTTGCAG
















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|86502916|gb|CI145549.1|CI145549
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|66931443|gb|CX118291.1|CX118291
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|86501807|gb|CI144440.1|CI144440
EST:     GCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: GCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|58693667|gb|CK082354.1|CK082354
EST:     TGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: TGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|29615143|gb|CB620156.1|CB620156
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|29684278|gb|CB680553.1|CB680553
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|29642142|gb|CB647149.1|CB647149
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|29685648|gb|CB681923.1|CB681923
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|29684277|gb|CB680552.1|CB680552
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|29669725|gb|CB666000.1|CB666000
EST:     CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA
EST: gi|29668135|gb|CB664410.1|CB664410
EST:     CACTGCGGCTCTCACAGGATCACTATATTATGTGGCTTCTGCCCCGAAAG                         ATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATATTGGGCGAGAGA
genomic: CACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 69 (downstream exon)
Score: 38

GGCATGGTGCCTCCATTTGTTCCATTTGCTCAAACGTTTGCAGCAGCCATCACTGCGGCTCTCACAGGATCACTCTATTATGTGGCTACTGCCCCGAAAGgtgactctaa ... atgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaccaagtgtgacatatatatatacatgttgtgatatatttgtatgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG
               atatatatatacatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactctaatttgcatgcttttctgtttggaaggaagtggcattgattcttgaaaccaagtgtgacatatatatatacatgttgtgatatatttgtatgattgcagATCCTACTTATGTGGTGACACCAGCAATGCGTTCAAATACTGGGCGAGAGAATCTCAAGAAACTATTTGCAG

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