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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaatggtgcaagcagctaagcatcactctggtttgctgcacaatctactggatttgacacaagatggtgtttgatttgtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG

Basic information

species Oryza sativa
transcript LOC_Os01g50770.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G436835_T01 (Zea mays), 3'ss of exon 4
gtaagtaatggtgcaagcagctaagcatcactctggtttgctgcacaatctactggatttgacacaagatggtgtttgatttgtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG
    ||||    ||||      ||| |   ||   ||||| || || |      |||||||| | ||  ||| | |   || |||    |||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| || || ||||| ||||| ||||| ||||| |||||||||||||
----gtaa----gcaaattttcaagtacttcttctgtttgatgtacgactgttgggatttgagagaa--tggggctcatttcgtgtggacagTATGAGTTGCTCGATGAGATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAGATATTGAGTGAGTTCATCAAGACAGATGCATACAGGATGGAGG

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G436835_T03 (Zea mays), 3'ss of exon 1
gtaagtaatggtgcaagcagctaa-gcatcactctggtttgctgcacaatctactggatttgacacaagatggtgtttgatttgtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG
         || | |   |   |  |  |   ||  |   | ||||     ||| ||||  ||    | |  | ||   |    || | |    |   | ||  | ||| |     |||    ||| | ||    |||| | ||    ||                                           
-----cggaggcgaagatattgagtgagttcatcaagacagatgca-----tacaggatg-gaggtcacacagcgtcc-acccatggccgtgacaaatgctgtgtcatgga-----gGAGCGAGGGGATCC--GGTACAAGAAGAATGAA-------------------------------------------

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G162145_T01 (Zea mays), 3'ss of exon 3
gtaagtaatggtgcaagcagctaagcatcactctggtttgctgcacaatctactggatttgacacaagatggtgtttgatttgtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG
            | |||||  |    |  |||   ||||| ||  |  |     ||| |||||  ||   || |     ||||||| | |||||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||| ||||||| ||||| ||||| |||||||||||||||||||
------------gtaagcaaatttcaagtacttctgtttgatgtgcggttactgggacttgacggaatggggcgcccattttgtgcttacagTATGAGTTGCTGGATGAGATGATGGATTTCGGGTACCCACAATACACGGAGGCGAAGATCCTAAGTGAGTTCATCAAGACAGATGCGTACAGGATGGAGG

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0225g00220.t01 (Vitis vinifera), 3'ss of exon 3
-gtaagtaat--ggtgcaagcagctaagcatcactctggtttgctgcacaatctactggatttgacacaagatggtgtt--tgatttgtgcctgc---agTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG
 ||   | ||  |||||    |   ||       | ||  |    | |   |  |    |  |   |  | ||  |  |  || ||||||| |     ||||||||||||||||||| |||||||| ||||| ||||| || || || || || || ||  | |||||||| || ||||| ||||| || |||||||| |
tgtctctcatttggtgcctttaataaattcgttttatgcgtaaaagaaagcttaatgaaaaattctatgaaattatactgatgctttgtgcttttcttagTATGAGTTGCTTGATGAGATGATGGACTTTGGTTACCCTCAGTATACTGAAGCAAAGATTCTGAGTGAATTTATCAAGACTGATGCTTATAGGATGGAAG

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S328_56V6.1 (Physcomitrella patens), 3'ss of exon 5
----gtaagtaatggtgcaagcagctaagcatc-actctggtttgct----gcacaa-------tctactggatttgac--acaagatggtgtttgatttgt------gcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG
    |||   ||       || |  | | |||| | | | ||||  |    | | ||       ||| |  | |||  |   ||||    |  ||| | |           ||||||||||| | || || || |||||||||||||||||||| ||||| ||||| || |||||  | |||||||| || ||||| ||||| || || ||||| |
gtaagtacaaaaaacgttgagaatttcaacatctattattgttttttctttgtaaaagtgggtttcttcgcgttttatcctgcaagtaaattcttggtctaacttttaatttgcagTATGAGCTTCTGGACGAGATGATGGATTTTGGGTACCCCCAATATACGGAAGCTAAAATTCTGAGTGAATTTATCAAGACTGATGCCTATAGAATGGAAG

upper sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S300_7V6.2 (Physcomitrella patens), 3'ss of exon 5
------gtaagtaatggtgcaagcagctaagcatcactctggtttgctgcacaatctactggatttgacacaagatggtgtttgatttgtg---cctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG
      ||   |||  ||||    |  || ||      |||  | |  |  |  |     ||||| |  | ||  |      | |||  ||   | ||||||||||| | ||||| || |||||||||||||| || || |||||||| || || |||||  | || || ||||| || || || || |||||||||||||
tttgttgtctttaagagtgctttaatttatgctctgtgctg-ctagaagtccttttctggggattggtaataatctaacaaattattcttgaatcatgcagTATGAGCTTCTTGACGAGATGATGGATTTTGGATATCCTCAATACACAGAAGCTAAAATTCTGAGCGAGTTCATCAAAACCGACGCATACAGGATGGAGG

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|27576432|gb|CA999126.1|CA999126
EST:     ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG                         TATGAGTTGCTTGATGAAATGATGGATTTTGGG
genomic: ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTGgtaagtaatg ... gtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGG
EST: gi|33793248|gb|CF322504.1|CF322504
EST:     ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG                         TATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAG
genomic: ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTGgtaagtaatg ... gtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAG
EST: gi|58673470|gb|CK062156.1|CK062156
EST:     ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG                         TATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAG
genomic: ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTGgtaagtaatg ... gtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAG
EST: gi|58665060|gb|CK053746.1|CK053746
EST:     ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTG                         TATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAG
genomic: ATTTCGAAGAGTTGGAGGAAGAGTCGCTGAGGGATAACTTTGTCGTTGTGgtaagtaatg ... gtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgcacaatctactggatttgacacaagatggtgtttgatttgtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG
                                     tttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaatggtgcaagcagctaagcatcactctggtttgctgcacaatctactggatttgacacaagatggtgtttgatttgtgcctgcagTATGAGTTGCTTGATGAAATGATGGATTTTGGGTACCCACAATACACGGAGGCGAAAATCTTAAGTGAATTCATTAAGACGGATGCGTACAGGATGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG