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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactgattggctattatcgtttttggctcatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 50
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 50
lower sequence: GRMZM2G068755_T01 (Zea mays), 5'ss of exon 51
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatttcaatcctggaggtgtttaag-ctagttttggtgtttttaactgattggctattatcgttt--ttggctcatgcag----------------
||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||||||||||  |  ||| || ||  || |     |  | |  ||| || |||    ||  ||    ||  |||    |||  | |   |                 
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCGTTTAGAACCTATATCAGAGATGGCCTAGCTCAGgtttgtaacctcagtcatgttggggcggggggttgggcttgttgctttgttatggatgttgtttgacgtacgattgatttaattacattgtttgtaatgcag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 50
lower sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 33
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactgattggctatta---tcgtttttggctcatgcag-----
||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||| |  || ||| |  |||||| |||| |||| ||| |  |  ||||   |||    | |||    |   ||  |     ||||      
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaatgcag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 50
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 53
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgttt-gctatttcaatc------ctggaggtgtttaagctagttt-----tggtgtttttaac--tgattggctattatcgtttttggctcatgcag-----------------------------
||||| ||||||||||||||||| ||||| ||||| |||||| | ||||| || |||||||| || |||||||||  | || || | |       |   | ||  ||||   |  ||     | || ||| || |   ||||||   |  | |  ||  |    ||                                
GTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaatttacttgtattaccacatgttcttaattgaacttgcattttgtatttctaccggcgattgggagtagtagaattgagtatttgaccattggcaattgattttaacattttggcag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 50
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 52
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgttt-gctatttcaatcctggaggtgtttaagctagttttggtgtttttaactgattggctattatcgtttttggctcatgcag--------------------------------------------
||||| ||||||||||||||||| ||||| ||||| |||||| | ||||| || |||||||| || |||||||||  | || || | |  |         |   ||   || | | ||      ||  |  |||  | || ||  |  |  |  |                                             
GTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcag

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 50
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 22
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatttcaatcc------tggaggtgtttaagctagttttggtgt-ttttaactgattggctattatcgttt-------ttggctcatgcag
|||||||||||||| ||||| || ||||| ||||| || ||| | || |||||||| |||||| |||| ||||| |||  ||  |||        || |  |        ||   | |||   |||||||     |  | || || |||       || | |  |||||
GTTGATATATTTGCGCAGCTCCAAAATGCTAGTGAGGCGTTTCGGACTTATATCAGGGATGGGTTAGCCCAGgtctgcatttagaatatccaaattgaaaattccaggattacaatgggtacattttaacaagcagtttcttttcttttcctcctttttgttgttgcag

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|58658439|gb|CK047119.1|CK047119
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58601380|gb|CK011908.1|CK011908
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCA
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCA
EST: gi|58675157|gb|CK063844.1|CK063844
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|218497579|gb|FG955134.1|FG955134
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58677253|gb|CK065940.1|CK065940
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCC
EST: gi|58690696|gb|CK079383.1|CK079383
EST:     AGAATGCAAGTGAAGCATTTAGGACCTATATCAGAGATGGGCTAGCTCAG                         GTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCC
genomic: AGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatt ... gctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactgattggctattatcgtttttggctcatgcag

- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA