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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcctgtcactacacagccttcaaataattcatggttccacatccataaacttgtgtatatatttgtgcactcttagtgaactcaatgaactgtacttagagctcagttttggtctttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGCGATCAGTATTGAGGGTACTCTAGCTGGAATTCTTGCATCGATAATTCTT

Basic information

species Oryza sativa
transcript LOC_Os01g52864.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52864.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G166383_T02 (Zea mays), 3'ss of exon 2
-----gtaagattcc------tgtcactaca--cagccttcaa-ataattcatggt-tccacatccataaacttgt-----gtatatatttgtgcactcttagtgaactcaatgaactgtacttagagctcagttttggtctttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGCGATCAGTATTGAGGGTACTCTAGCTGGAATTCTTGCATCGATAATTCTT
      | ||||| |        |||||| |  |||||||||  | | |||||  | |  || |||||    ||||     | | || | | || | |  || |    ||     |||| |     |  | | | |||||  || |||||| ||||||||||||||||||| | |||||||||||  |||||||||||||||| |||||||||||||||||| | ||||||||||| || ||  |  |||  
gtaagtttagatttcgtaacacatcactatatgcagccttcattagatttcatcatgtaaacttccattcttttgtagaatgcaaatctatatggagttataataggttctcaatactgaat----acttaaatcttggttcttctgtagAATAGGTACCTGGTGACAACATTAAAGGTTGTTCCTAGAGGTACAGAAGGTGCAATCAGTATTGAGGGTACTATTGCTGGAATTCTAGCGTCTGTGTTTC--

upper sequence: LOC_Os01g52864.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G166383_T03 (Zea mays), 3'ss of exon 1
-----gtaagattcc------tgtcactaca--cagccttcaa-ataattcatggt-tccacatccataaacttgt-----gtatatatttgtgcactcttagtgaactcaatgaactgtacttagagctcagttttggtctttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGCGATCAGTATTGAGGGTACTCTAGCTGGAATTCTTGCATCGATAATTCTT---
      | ||||| |        |||||| |  |||||||||  | | |||||  | |  || |||||    ||||     | | || | | || | |  || |    ||     |||| |     |  | | | |||||  || |||||| ||||||||||||||||||| | |||||||||||  |||||||||||||||| |||||||||||||||||| | ||||||||||| || ||  |  |||||   
gtaagtttagatttcgtaacacatcactatatgcagccttcattagatttcatcatgtaaacttccattcttttgtagaatgcaaatctatatggagttataataggttctcaatactgaat----acttaaatcttggttcttctgtagaatagGTACCTGGTGACAACATTAAAGGTTGTTCCTAGAGGTACAGAAGGTGCAATCAGTATTGAGGGTACTATTGCTGGAATTCTAGCGTCTGTGTTTCTTGCA
















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|25803882|gb|CA759843.1|CA759843
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         ---GTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
EST: gi|88847576|gb|CI016069.1|CI016069
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         TAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
EST: gi|86259218|gb|CI010519.1|CI010519
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         ---GTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
EST: gi|86496138|gb|CI138771.1|CI138771
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         ---GTACCTGGTGACAACACTAAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
EST: gi|89189983|gb|CI013550.1|CI013550
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         ---GTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
EST: gi|29658377|gb|CB654652.1|CB654652
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         A
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagag-
EST: gi|29658377|gb|CB654652.1|CB654652
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         A
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagag-
EST: gi|29658377|gb|CB654652.1|CB654652
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         A
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagag-
EST: gi|88839669|gb|CI015760.1|CI015760
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         ---GTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
EST: gi|58693851|gb|CK082538.1|CK082538
EST:     CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         ---GTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: CTAAGTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
EST: gi|88209808|gb|CI209657.1|CI209657
EST:     GTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAAC                         ---GTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC
genomic: GTGACACAGTTTCCAGTGAAATAGGGAAGGCCTACGGAAGAACAACgtaagattcc ... ttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttagtgaactcaatgaactgtacttagagctcagttttggtctttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGCGATCAGTATTGAGGGTACTCTAGCTGGAATTCTTGCATCGATAATTCTT
                                          tctttttgt  CT-rich tract
                                            tttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattcctgtcactacacagccttcaaataattcatggttccacatccataaacttgtgtatatatttgtgcactcttagtgaactcaatgaactgtacttagagctcagttttggtctttttgtagagTAGGTACCTGGTGACAACACTTAAGGTTGTTCCGCGAGGTACAGAAGGTGCGATCAGTATTGAGGGTACTCTAGCTGGAATTCTTGCATCGATAATTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA