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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g25580.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
| | | ||  | |      ||   | ||     ||     |  ||||     | |||| || | |||   || |       |||   ||    | | |||||| |  |||||  |||| |  |||||||| |||||||||||||| ||||||||||||||||| ||||||||||| |||||||| || |||||||||
actgacttccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG

upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaat---gttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
 ||||  |   | |  || |   |||  |||      |||  ||  ||||   ||||| | | ||  |   | |   | ||||  |  ||||  | |||  || | | |  | || || || |  || ||  | ||||  || |||||||| |||||||||||||| || |||||||| ||||| || || ||||| |||
-tttagctaagcctagatttattgtttgatggaagtgtttctttattaatctagttctcgtcataacaaactta-aattattgaattttgttgtatttat-agTAGTAGCAGTGAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG

upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G03970.1 (Glycine max), 3'ss of exon 13
-------atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
       ||||| |    | |  || |  | ||  ||  ||  |||   | | || |     | |      | |||||    | ||||||    | ||       |||  | | || || || || |  || || || ||||| ||||||||||| |||||||| ||||| || |||||||| ||||| || || ||||| |||
ttgtaaaatttaatgaagcctagatctgtaatt-tatatgtttattcattatctagttactgtcatcataaactttaaacaactttgcttttcatcta------tagAGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
-atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaatta--ccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
  || |||     |||  | || |     |  | ||   | ||||| |  | || |  | ||| | |  | ||   | || |   |  ||  | ||     |||  | | || || || || |  || || ||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| || || ||||| |||
ccttcattcatgaatggtttttcaa--aaaccattcttatatgtttatt-tattatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
atttatttggacatgtatgttgagttgcatgag---tccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
 ||||  |   | |  || |   |||  |||     |    ||| ||  |   ||||| | | ||  |   | |   | ||||  |  ||||  | |||  |||| | |  | || || || |  || ||  | ||||| ||||||||||| |||||||||||||| || |||||||| ||||| || || ||||| |||
-tttagctaagcctagatttattgtttgatggaagttttgatttattcatctagttctcgtcataacaaactta-aattattgaattttgttgtatttat-agAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
atttatttggacatgtatgttgagttgcatg----agtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
  |||  |     | || |||||  |   ||    | |  |||| ||| |  | ||   |    | |  |||| ||     ||| || |   ||   ||   |||  ||| |  ||| | || |  ||||||||||| || |||||||||||  | ||||||||||| || |||||||| ||||| ||||| || || |||
-cttacatta--ctctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactctttt-ttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG

upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattg--cttcatgtttaa--attac-cagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
|| ||| |        || |   |||  ||   || | || | |   | |||  |      | || |  |       ||   ||  || ||||    |||   |||  ||| || ||  | || |  || || |||||||| |||||||||||| | ||||| || || || ||||||||||||||||| || |||||||||
atgtatctttgtg---atatctggtta-atctttctactt-gatgccagtgtattcagaccagtaatccaggatgtgttaacctaaatatttatctgttatgtagAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAG

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|29626795|gb|CB631806.1|CB631806
EST:     ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAG                         AACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
genomic: ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAGgtctgtgcat ... aaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
EST: gi|218485563|gb|FG949368.1|FG949368
EST:     ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAG                         AACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
genomic: ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAGgtctgtgcat ... aaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
EST: gi|58680727|gb|CK069414.1|CK069414
EST:     ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAG                         AACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
genomic: ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAGgtctgtgcat ... aaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
EST: gi|58674876|gb|CK063563.1|CK063563
EST:     ATGAGCAATTTTGTGTCCAAGAATCCAGCTGCTCAACTGCAGCAAGCAAG                         AACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
genomic: ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAGgtctgtgcat ... aaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
EST: gi|58675734|gb|CK064421.1|CK064421
EST:     GTGTCCAAGAATAAAGCTGATCAACTGCAGCAAGCAAG                         AACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
genomic: GTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAGgtctgtgcat ... aaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
EST: gi|66914840|gb|CX101688.1|CX101688
EST:     ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAG                         AACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT
genomic: ATGAGCAATTTTGTGTCCAAGAATAAAGCTGCTCAACTGCAGCAAGCAAGgtctgtgcat ... aaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG
                    ttttaat  putative branch site (score: 3)
      ttcttgacttattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC