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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaatgtgtttgtttggtgacatactgacatgcattatacagtgttgcaattaggcccggcgaaaaacgtgtagtaattatttgctctttttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGG

Basic information

species Oryza sativa
transcript LOC_Os03g08550.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G330907_T01 (Zea mays), 3'ss of exon 1
gctaatgtgtttgtttggtgacatactgacatgcattatac-agtgttgcaattaggcccggcgaaaaacgtgtagtaattatttgctctttttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGG
    ||| || |  ||| |               || |    ||  |||  || |  |    |  |  || |||  |||||| |||| || |  |||||||||| ||||||||||||||||||||| || ||||||||||| |||||||||| || ||||||||| | ||| || || ||||||||||| |||||||||||
atctatgcgtattcttgctacttcgagtttgcaaatgaactgagatttgtgatgacacattccctagcac-tgttctaattagttgcactctcacatgcagTTAATGTCCTCAATACGCTCTTCACCAGTCTGAATTCTCCTGGGCAGCTCAGAGCTTGGCAGGCGAATGGCGGTGATCCTTGTGGCCAGTCATGGCAGGG

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G153393_T01 (Zea mays), 3'ss of exon 1
-gctaatgtgtttgtttggtgacatactgacatgcattatacagtgttgcaattaggcccggcgaaaaacgtgtagtaattatttgctctttttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGG
     || |  ||| |   | |  |    | ||| | |      | |  ||   |   ||      | || |||  |||||  |||| || |  ||||||||||  |||||||| ||||||||||| || ||||||||||| |||||||||| |||||||||||| | ||| || || ||||||||||| |||||| ||||
tatgcatattcttgatacttcaagtttgcaaatggactgagatatctgacagacacatcccctagtatac-tgttctaatttgttgcactctcgcatgcagTTAACGTCCTCAACACGCTCTTCACCAGTCTGAATTCTCCTGGGCAGCTCACAGGTTGGCAGGCGAATGGGGGTGATCCTTGTGGCCAGTCATGGAAGGG
















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|88426314|gb|CI574197.1|CI574197
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATAAGCTCTTCAATAGCCTGAATTCTCCGGGGCAGCTCC
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88308468|gb|CI650877.1|CI650877
EST:     CTGGCCCCANAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88334914|gb|CI648689.1|CI648689
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88447803|gb|CI576999.1|CI576999
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGAAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGGAGTTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88342558|gb|CI637134.1|CI637134
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88364714|gb|CI612529.1|CI612529
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88311044|gb|CI657957.1|CI657957
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAG
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAG
EST: gi|88309648|gb|CI656389.1|CI656389
EST:     TTGGCCCCAAAACCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGGTC-TCAATACGCTCTTCANTAGCCTGAATTCTCCGGGGCAGCTC
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTG-TCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTC
EST: gi|88340041|gb|CI650488.1|CI650488
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAG
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAG
EST: gi|88764540|gb|CI773658.1|CI773658
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88317279|gb|CI627928.1|CI627928
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGAACCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTACCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|29635613|gb|CB640622.1|CB640622
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88388037|gb|CI590313.1|CI590313
EST:     TTGGCACCAGAAGCAAATCTTGGTCGCTGCAGACAC-GACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCTAGCT-
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGC-AGCTC
EST: gi|88364126|gb|CI610470.1|CI610470
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88354919|gb|CI615800.1|CI615800
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATAGGCTCTTCACTAGCCTGAATTCTCCGGGGCAGGTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|87017160|gb|CI286296.1|CI286296
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCT
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCT
EST: gi|88354679|gb|CI613957.1|CI613957
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88398743|gb|CI598708.1|CI598708
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88308055|gb|CI647882.1|CI647882
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88362471|gb|CI623811.1|CI623811
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88359221|gb|CI617886.1|CI617886
EST:     TGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCCTAATGATG                         TTACTGTCCTCAGTACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCC-TAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88428399|gb|CI564867.1|CI564867
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATG                         TTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCA
EST: gi|88424166|gb|CI581721.1|CI581721
EST:     TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACACTAATGATG                         TTACTGGTCCTCAATACGCTCTTCACTAGGCGTGAATTCTCCGGG
genomic: TTGGCCCCAGAAGCAAATCTTGGTCGCTGCAGACACCGACCCTAATGATGgtaagctaga ... tttcatgcagTTACTG-TCCTCAATACGCTCTTCACTAGCC-TGAATTCTCCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaattaggcccggcgaaaaacgtgtagtaattatttgctctttttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGG
                                 ttatttgctctttttc  CT-rich tract
                         tgtagtaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaatgtgtttgtttggtgacatactgacatgcattatacagtgttgcaattaggcccggcgaaaaacgtgtagtaattatttgctctttttcatgcagTTACTGTCCTCAATACGCTCTTCACTAGCCTGAATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
gctaatg
- - - -tgtttgt
- - - - - - - - - - -catactg
- - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - gtgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaac