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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatgaaccctctcttgttgtgcatccatccacgggacgggacacatgaaaacatcatcatctcataaattaataatttatgtggctatattcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g51670.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51670.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G038598_T02 (Zea mays), 3'ss of exon 6
-------------------------------gtatatatgaaccctctcttgttgtgcatccatccacgggacgggacacatgaaaacatcatcat-ctcataaattaataatttatgtggctatattcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG
                                 ||  |  |  |  |   ||||||  |  ||  ||     | |||        |  ||  | || |||||  ||   |    | ||       || | |  ||| ||||| ||||||||  |||| |||||||||||||| || ||| |||||||||| || ||||||||||| |||||||| |||
gttggttattaccggttgtttattctgaacttcatggacaactcagccgctgttgtatactcaagcaatcagctggagctggctgatgatgctgatgctcatctatcggttgggtgtg-------atgcgtgtagGCTGTGAAGTGTACAACTTGGGGACTGGAAAGGGGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAG
















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|218494764|gb|FG965511.1|FG965511
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAA                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
EST: gi|218481702|gb|FG969560.1|FG969560
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
EST: gi|33681007|gb|CF309246.1|CF309246
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
EST: gi|218783417|gb|GE329469.1|GE329469
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
EST: gi|33679559|gb|CF307798.1|CF307798
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGA-GGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAA
EST: gi|29684846|gb|CB681121.1|CB681121
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
EST: gi|33661837|gb|CF292804.1|CF292804
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
EST: gi|33686980|gb|CF315219.1|CF315219
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GAATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGGA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGA-TGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAA
EST: gi|218482145|gb|FG968615.1|FG968615
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAG
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAG
EST: gi|218505351|gb|FG968507.1|FG968507
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
EST: gi|218498936|gb|FG953341.1|FG953341
EST:     TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAG                         GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA
genomic: TGGTCATATCGCCGCGTTAAGGAAGCTCTATGAAGATTCTGATAGAATAGgtatatatga ... attcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaaaacatcatcatctcataaattaataatttatgtggctatattcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG
                       aattaat  putative branch site (score: 3)
                                            tattcttcc  putative PPT
         atcatcatctcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatgaaccctctcttgttgtgcatccatccacgggacgggacacatgaaaacatcatcatctcataaattaataatttatgtggctatattcttccagGATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG

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