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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttactagttatataccgtaggaaagctaatgtgatgtttcccttggcgtgaggcgtatttatttcagcaacagtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC

Basic information

species Oryza sativa
transcript LOC_Os01g58114.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 3
--tttactagttatataccgtaggaaagctaatgtgatgtttccct-tggcgtgaggcgtatttatttcagcaacagtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC
    || | |   |      |    ||  || ||   | ||||  | ||   ||  ||   |  | |    ||| | ||||||||||     |   ||  |||||||||||| ||||||||||| |||| ||||| ||||||||||| |||||||| | ||||||||| || ||||||||||||||| | || ||||||||||
taccta-tggcactgggttctctccaatgtagtgcactatttctttatgagctggagcagttccaatgtc-caaaattaagctaacaaatggtggattg-cagGGAGAAGATGTTATTGCTATCCTGCCCTGGGAGGAATGGTGGGAGTTTGAAGTGACAAAGGATGACTCAAATCCTCAGATTGCACTGCTTCCTTTGCATC

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G45930.1 (Glycine max), 3'ss of exon 3
tttactagttatataccgtaggaaagctaatgtgatgtttcccttggcgtgaggcgtatttatttcagcaaca-gtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC
 | |  | | ||      |    |      ||| |  | | |   ||| |  || ||     |    |||     |   ||  |   | ||   ||| |||||||||||||| |||||| |  | ||||||||||| ||||||||||||||| | || || |||||||||||||| || |||||  | || || ||||| |
-tgagaaatgatggtaaatgtatagtggtttgtcaactctgcagcggcatttggggtcaagttgctggcattttattttcttcctcaccttttgtttgcagGGAGAAGATATAATTGCTGTGATACCATGGGAAGAGTGGTGGGACTTTGAACTGAATAATGATGATTCCAATCCCCATATTGCTCTGCTTCCATTGCACC

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA14G02820.1 (Glycine max), 3'ss of exon 3
-tttactagttatataccgtaggaaagctaatgtgatgtttcccttggcgtgaggcgtatttatttcagcaaca-gtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC
   |  ||    ||||    |     | |  ||| |  | |     ||| |  || ||     |   ||||     |   ||  |   | ||   ||| |||||||||||||| || ||| |  | ||||||||||| ||||||||||||||| | || || |||||||||||||| || |||||  | || || ||||| |
tgatggtaaaagtatagtccatagtggtt--tgtcaactctgtagcggcatttggagttaagttgctagcattttatttcctgcctcaccttttgtttgcagGGAGAAGATATAATAGCTGTGATACCATGGGAAGAGTGGTGGGACTTTGAACTGAATAAAGATGATTCCAATCCCCATATTGCGCTGCTTCCATTGCACC

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G54870.1 (Arabidopsis thaliana), 3'ss of exon 3
tttactagttatataccgtaggaaagctaatgtga--tgtttcccttggcgtgaggcgtatttatttcagcaacagtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC
                 |||  ||    | |   |  || | ||||     | ||  | |    |||     |   | |  |    |   ||  | |   ||||||||||| | || || ||||| |||||||| || |||||||  ||||||  || ||||||||| || ||||||||||||||| | |||||||||||||
-----------------gtaacaacaacacttcaaagtgctgccctaaagttaagttgcaagattttttttga---tgaagtttttttttttcttgtcatagGGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAACAAACAAAGGATGACTCGAATCCTCAGATTGCACTGCTACCTTTGCATC

upper sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G27020.1 (Arabidopsis thaliana), 3'ss of exon 3
---tttactagttatataccgtaggaaagctaatgtgatgtttcccttggcgtgaggcgtatttatttcagcaacagtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC
      |||  || | |    | | |  ||   | || |  ||   ||   |     | |  || |||  ||     |   ||  |   | ||    |   ||||||||||| | || || || |||||||||||||| |||||||| ||||||  ||  |||||||| || ||||| || |||||||| ||||| |||||||
gtggaaactgattct-tttaatggaactgcatttttgttccttttttttatgcatatcatgatt-ttttggctgtcttctcctt-cgaacctttgggtcatagGGAGAAGATGTAATAGCGATATTGCCATGGGAAGAGTGGTGGGAGTTTGAACAAACCAAGGATGACTCGAATCCCCACATTGCATTGCTACCGTTGCATC

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|218493202|gb|FG958053.1|FG958053
EST:     ATTCTGAAGGAAAGC-TTGGGTTGGGGAATCTGGTCATGAGAATGAACA-                         GGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAA
genomic: ATTCTGAAGGAAAGCTTTGGGTTGGGGAATCTGGTCATGAGAATGAACAGgtagtggtca ... aatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAA
EST: gi|58655987|gb|CK044667.1|CK044667
EST:     ATTCTGAAGGAAAGCTTTGGGTTGGGGAATCTGGTCATGAGAATGAACAG                         GGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAA
genomic: ATTCTGAAGGAAAGCTTTGGGTTGGGGAATCTGGTCATGAGAATGAACAGgtagtggtca ... aatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAA
EST: gi|25797971|gb|CA753932.1|CA753932
EST:     ATTCTGAAGGAAAGCTTTGGGTTGGGGAATCTGGTCATGAGAATGAACAG                         GGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAA
genomic: ATTCTGAAGGAAAGCTTTGGGTTGGGGAATCTGGTCATGAGAATGAACAGgtagtggtca ... aatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgtgaggcgtatttatttcagcaacagtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC
                                               tttttc  CT-rich tract
                                      atgcattaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttactagttatataccgtaggaaagctaatgtgatgtttcccttggcgtgaggcgtatttatttcagcaacagtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG