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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgctatatatttctatcttctactatttaaattcataaatatttgatgagtttcagcaattaaatttgaaaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 8
gtaatttgctatatatttctatcttctactatttaaattcataaatatttgat---gagtt-tcagcaattaaatttgaaaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG
|||| || ||||   |  ||      ||   |||  | | |   || ||  |     | || |||  || || |||| |||| || ||| | ||| |   |||| || ||||||||||| |||||||||||||||||| ||||| | |||||||| ||| |||| || || |||||
gtaaatttctatccgtcacttaaacatagc-tttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaactacagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 16
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 17
-----gtaatttgctatat---atttctatcttctactatttaaatt-cataaatatttgatgagtttcagcaattaaatttgaaaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG
        |  | ||  ||   |  |   ||||  ||||   ||| |  |  || | || |    ||||||    ||||    |  |  | ||| | |||||   |||| || ||||| ||| | ||||||||||| |||||| ||||| |||| ||||| |||||||||||||| || ||
gtataaacacctactgcattggaaattcctctttcactaaccaaagtgtaccaaaagtttaattatttcag----taaaacgtattattttcagGAAAGAGGTGATTGATGAAGATGGATGGCTTCACACTGGAGATATAGGTCTGTGGCTGCCGGGAGGACGTCTAAAAATTATTGACAG
















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|29630787|gb|CB635796.1|CB635796
EST:     TAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: TAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
EST: gi|568356|gb|D39204.1|D39204
EST:     GTTAGGGG-CCTACGATATTCTGTGGTTACTATAAAGACGGAATCCAAAC                         TAGAGAGGCTGTTGACGAGGNTGGGTTGGT-ACACACTGGAG
genomic: GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGG-TTGGTTACACACTGGAG
EST: gi|58659745|gb|CK048425.1|CK048425
EST:     GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     GGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: GGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAAC                         TAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT
genomic: GTTAGGGGACCTACGATATTCTGTGGTTACTATAAAGACGAAATCCAAACgtaatttgct ... aaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaaattcataaatatttgatgagtttcagcaattaaatttgaaaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG
                atttgat  putative branch site (score: 5)
     aattcataaatatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgctatatatttctatcttctactatttaaattcataaatatttgatgagtttcagcaattaaatttgaaaacctgcagTAGAGAGGCTGTTGACGAGGATGGTTGGTTACACACTGGAGACATAGGTTTGTGGATGCCTGGAGGGCGTCTAAAAATTATAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG