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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtcatcagtttctgaatcctgtattttcactttcatcctttcctaccaataggatttgctcttgatcatgatgttcagatggtctgctttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCGATGTATGCATTGCTGAGATCAAGTGAACAGCCTCCTA

Basic information

species Oryza sativa
transcript LOC_Os03g31550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G888877_T01 (Zea mays), 3'ss of exon 2
----------atgtcatcagtttctgaatcctgtattttcactttcatcctttcctaccaataggatttgctcttgatcatgatgttcagatggtctgctttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCGATGTATGCATTGCTGAGATCAAGTGAACAGCCTCCTA
          | || || |   | |   |    |   ||||  |   ||||||||||||  |     || |||||  | || ||      ||| ||||| | |||| |||||| ||||||||| ||| || ||||||||||||||||||||||||||||||||||||||||| ||||||||| |||||||||| ||  |||||||||| |
attgtttactaagtaataaagctgt---tttcatgcattcaggtcgttcctttcctacctgtgcaccttcctctt--ttatcata-----atgctctgcctcccttgcagGAATGTTTAGCCAAGGCACATGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCTATGTATGCACTGCTGAGATCTAGCAAACAGCCTCCCA

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------------atgtcatcagtttctgaatcctgtattttcactttcatcctttcctaccaataggatttgctcttgatcatgatgttcagatggtc--tgctttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCGATGTATGCATTGCTGAGATCAAGTGAACAGCCTCCTA
                                                                                           ||||  |   | ||  |  | ||   | | |  ||  | |||   |   | |   |||| | |   ||||  |  || |  |   |  ||   ||  | ||||||    | ||   ||| || |||||||||||||||||||| || ||||||||||| ||||| |||||||||||  |  | |||||| ||   || ||||
gtgacatactgtcttcttttatcatgcatatgtactagtattacttgctattgttttgagtatcctttacttgtttggttctcatggtgtaatgt-gtttatctccaagccttgggatatgagctttcttcttattttaaatttatatttaccc---atcaatactttgaatttacccttgtaatctcttcagGAATCCCTGGCTCGGGCTCATGGTTCACAATGTGGATTTTGTACTCCTGGTTTTGTTATGTCCATGTATGCATTATTACGGTCAAGTCAAACACCACCTA

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------------------atgtcatcagtttctgaatcctgtattttcactttcatcctttcctaccaataggatttgctcttgatcatgatgttcagatggtctgctttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCGATGTATGCATTGCTGAGATCAAGTGAACAGCCTCCTA
                                                                                                 ||||  |   | || |   | ||  | |   ||||| || | |  ||  | |   |||| | | | |  |   ||     |     ||   ||  | ||||||    | ||   ||| || |||||||||||||||||||| || ||||||||||| ||||| |||||||||||  |  | |||||| ||   || ||||
gtgacagatgctcagactatcatcttttatcatgcttgtgtacttgttacatgctattgttttgagaatccattacttgtttgcttcccatggtgtaatgt-gtttatctccgggccttggctatgagctttcttcttattttaa-atttatatttacccatcaatactgtgaatttacc-cttgtaatctcttcagGAATCCCTGGCTCGGGCTCATGGTTCACAATGTGGATTTTGTACTCCTGGTTTTGTTATGTCCATGTATGCATTATTACGGTCAAGTCAAACACCGCCTA

upper sequence: LOC_Os03g31550.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 3
atgtcatcagtttctgaatcctgtattttcactttcatcctttcctaccaataggatttgctcttgatcatgatgttcagatggtctgctttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCGATGTATGCATTGCTGAGATCAAGTGAACAGCCTCCTA
                           |    ||| |    ||||      |    |||  |||   |  ||   | |  ||  ||    || ||  |||||    || ||     | || ||||| |||||||| ||||| || || |||||||| |||||||||||||| ||| |||| |||||| || |  | ||| 
--------------------------gtggggttttacttcttccagatttt----ttttttctcatttctgcgatcctaattctccctatttctctcagGAGTCATTGGCATCTTCGCATGGTTCTCAATGTGGGTTTTGTACTCCCGGTTTTGTCATGTCGATGTATGCCTTGTTGAGGTCAAGTAAAAACTCACCTT

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|88367173|gb|CI563937.1|CI563937
EST:     TCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCAATCCAG                         GAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGT
genomic: TCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCAATCCAGgtgatgctct ... ttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGT
EST: gi|88368103|gb|CI574985.1|CI574985
EST:     TCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCAATCCAG                         GAACGTTTAGCCATGGGCCCACGGT
genomic: TCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCAATCCAGgtgatgctct ... ttccttacagGAACGTTTAGCCATGG-CCCACGGT
EST: gi|88421291|gb|CI569136.1|CI569136
EST:     CACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCCAATCCAG                         GAACGTTTAGCCATGGCC-AGGGTTCA-ACTGTGGATTTTGC-CCCCTGGT
genomic: CACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCC-AATCCAGgtgatgctct ... ttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGT
EST: gi|88353883|gb|CI634674.1|CI634674
EST:     TCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCAATCCAC                         GAACGTTTAGCCATGGCCC
genomic: TCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCAATCCAGgtgatgctct ... ttccttacagGAACGTTTAGCCATGGCCC
EST: gi|88411227|gb|CI564348.1|CI564348
EST:     TCACAGTACAGGGAATTGGGAATCGTCAGCGAGGTTTGCACC-AATCCAG                         GACCGTTTA-CCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGC
genomic: TCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCACCCAATCCAGgtgatgctct ... ttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGG-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaataggatttgctcttgatcatgatgttcagatggtctgctttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCGATGTATGCATTGCTGAGATCAAGTGAACAGCCTCCTA
                tcttgat  putative branch site (score: 4)
                                       tctgctttccttac  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtcatcagtttctgaatcctgtattttcactttcatcctttcctaccaataggatttgctcttgatcatgatgttcagatggtctgctttccttacagGAACGTTTAGCCATGGCCCACGGTTCACAATGTGGATTTTGCACCCCTGGTTTTGTGATGTCGATGTATGCATTGCTGAGATCAAGTGAACAGCCTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA