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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcccatacttctttatattggcaatttgtattgacatatttatatttaacttgtagcacatacattgaaaattattgacgagtcttatcttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCTCTTCATGTTAAGTCTGCTATGGCAGAACTCTCCCGATCTGAAAGAGGCG

Basic information

species Oryza sativa
transcript LOC_Os02g17500.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17500.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G412899_T01 (Zea mays), 3'ss of exon 3
---ctcccatacttctttatattggcaatttgtattgacatatttatatttaacttgtagcacatacattgaaaattattgacgagtcttatcttttatt-cagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCTCTTCATGTTAAGTCTGCTATGGCAGAACTCTCCCGATCTGAAAGAGGCG
     | |||    | |    |   |  | ||| |||| | |   |  |   | |||   |    | | |  |      ||| ||| | | | ||| | | |||||||||| ||  | |||||||||||| ||||||||||| ||| ||||||| |||||||| || ||||| ||||||||||| ||  ||| ||||||||  |
aagtacacattacccatacagtctcctgtgtgt-ttgataaaaaaaagt---atttgagacttccagactcgagtgatctgatgaggcctgtttttgaatgcagTGTGGAAAAATAAGTGAAGCAGAGATGCAATTTGAAAAGCTTTTAGGTCCCCTTCATGTAAAATCTGCCATGGCAGAACTTTCTAGATATGAAAGAGTAG
















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|29643521|gb|CB648528.1|CB648528
EST:     AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAG                         TGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
EST: gi|88362011|gb|CI607011.1|CI607011
EST:     AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAG                         TGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
EST: gi|218499348|gb|FG943597.1|FG943597
EST:     AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAG                         TGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
EST: gi|88827907|gb|CI778472.1|CI778472
EST:     GTGGCTGTATAAG                         TGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: GTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
EST: gi|88732502|gb|CI755679.1|CI755679
EST:     GTGGTTGTATAAG                         TGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: GTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
EST: gi|66922886|gb|CX109734.1|CX109734
EST:     AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAG                         TGTGGAAGAACAACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
EST: gi|218498315|gb|FG958350.1|FG958350
EST:     AAGCTCTTGGAATGGAGTTCTGCGCTGAGAGCCCCCAGTGGCTGTATAAG                         TGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: AAGCTCTTGGAATGGAGTTCTGTGCTGAGAGCCCCCAGTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
EST: gi|88827571|gb|CI778136.1|CI778136
EST:     GTGGTTGTATAAG                         TGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT
genomic: GTGGCTGTATAAGgtgtgtttat ... ttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaacttgtagcacatacattgaaaattattgacgagtcttatcttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCTCTTCATGTTAAGTCTGCTATGGCAGAACTCTCCCGATCTGAAAGAGGCG
                            tattgac  putative branch site (score: 2)
                                      tcttatcttttattc  putative PPT
               atacattgaaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcccatacttctttatattggcaatttgtattgacatatttatatttaacttgtagcacatacattgaaaattattgacgagtcttatcttttattcagTGTGGAAGAACGACTGAAGCAGAGATACAATTTGAAAAACTTCTAGGTCCTCTTCATGTTAAGTCTGCTATGGCAGAACTCTCCCGATCTGAAAGAGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG