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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattaaactggtgaaggtccattatatctattgcattttccttgcatgaactgtcttggaactgtcctttttttgtaactaatttctaaacaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGTTGCCAGTGTATTGGAGAGGAACAACTTGCCAGGCTCAATTTTTACAGCA

Basic information

species Oryza sativa
transcript LOC_Os09g26880.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 7
-tcattaaactggtgaaggtccattatatctattgcattttccttgcatga-actgtcttggaactgtcctttttttgtaactaatttctaaacaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGTTGCCAGTGTATTGGAGAGGAACAACTTGCCAGGCTCAATTTTTACAGCA
    || |||      |       | | |   | ||| |   |||||     || |    |   ||||   ||| |   |  |  || |   |   || |||||||||||||||||| |||||  ||||||||||||||||||| |||||||| || ||||||||||||| |||||||||||||||| ||||||||||| | 
tctgttcaacatactcaccagttctgttttagtggcaataaacttgctcagtaccgcagggaggctgttactttgtctaatgttgttgc--gattcttacagGAAAGGTGCTCCAACAACTCCACTGATCACTATTGCAATGACAAAAATAGTGGCTAGTGTATTGGAGAAGAACAACTTGCCAGGCGCAATTTTTACATCT

upper sequence: LOC_Os09g26880.4 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 8
tcattaaactggtgaaggtccattatatctattgcattttccttgcatgaactgtcttggaactgtcctttttttgtaactaatttctaaacaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGTTGCCAGTGTATTGGAGAGGAACAACTTGCCAGGCTCAATTTTTACAGCA
   | | | | || |      ||||    |            ||| ||    |   ||||    |    |  ||  ||  | ||   |         ||||||||||||||||||||| ||||| || ||||| |||||||| ||  |||| ||    || || ||||  |||||||| || ||  | |||||||| || 
gtttcataatagtaacacaatattaatcttgacaatgaaaatttgtattggtttgattggtgtagctaatacttaatacatcatacatgtgattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGTAGCTGAAGTTTTAGAGAAAAACAACTTACCCGGTGCCATTTTTACGGCC
















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|29668604|gb|CB664879.1|CB664879
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|29670252|gb|CB666527.1|CB666527
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|59930115|gb|AB178657.1|AB178657
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGAWGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|29673829|gb|CB670104.1|CB670104
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|29670274|gb|CB666549.1|CB666549
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|29668613|gb|CB664888.1|CB664888
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|59930145|gb|AB178687.1|AB178687
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTMATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|29668647|gb|CB664922.1|CB664922
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|29668563|gb|CB664838.1|CB664838
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT
EST: gi|59930143|gb|AB178685.1|AB178685
EST:     GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTG                         GAAAGGTGCTCCAACTACWCCGTTGAWCACTATTGCGATGACTAAAATAGT
genomic: GTTGGAATGCCTGCATAGCTTTGGTATGTGGAAACTGTGTTGTCTGgtaagaatga ... acaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaactgtcttggaactgtcctttttttgtaactaatttctaaacaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGTTGCCAGTGTATTGGAGAGGAACAACTTGCCAGGCTCAATTTTTACAGCA
                                       ttctaaa  putative branch site (score: 2)
                       tttttttgtaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattaaactggtgaaggtccattatatctattgcattttccttgcatgaactgtcttggaactgtcctttttttgtaactaatttctaaacaattgcagGAAAGGTGCTCCAACTACTCCGTTGATCACTATTGCAATGACTAAAATAGTTGCCAGTGTATTGGAGAGGAACAACTTGCCAGGCTCAATTTTTACAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA