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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattctgcaacatagagaatctagatattattctcgatagttttattggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
-----------------------aattctgcaacatagag---aatctagatattattct----cgatagttttattggcaatattaactatatgcttgttgacaa-gtgagt---gattgt---ttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
                        |   | ||| |||  |   | | |  |||| |   |     | | ||||  ||       |||   | | ||   |  | |   ||| |    ||| |    |  ||   ||||   | |||||||||||| ||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||| || |||
gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------aattctgcaacatagagaatctagatattattctcgatagttttattggc-aatattaactatatgcttgttgaca-agtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
                                                                     ||  |   |  | |    |  |  ||        || | ||  |||    |||||  ||  |   | ||||     | ||  | | | |  |    || ||| | || ||  | |||||  |||| ||||| ||||| || || |||||||| ||| | |||||||| || ||||| ||||| ||||||||||| ||||||
gtttgtcttagctgaattttatttctggtgtaatctaggtcttattaggaagcttttgttaatgaaatgatgttttcatgttgctttttaatttacatacaaggacatttccatttatgaatatgtacagtgatcctgtttgtgcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTAAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACTGCT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
--aattctgcaacataga---gaatctagatattattctcgatagttttattggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
  | || |    |||| |   ||    | | ||||   |  |||  | ||    |||  ||  || | | |||    |    |   | | | ||  | | |  ||| | || || |||||||||||||| ||||| ||||| || || |||||||| ||| |||||||||| || ||||| ||||| ||||||||||| || || 
taatttgtttggcatatacatgagagaaaaaattacctttcataaatata----caacttttcctgtttccttaactattgtttgttcaat-ttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------aattc---tgcaacatagagaatctagatattattctcgatagttttattggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
                                               ||||    ||  | | | |  |   | | ||||   |  |||  | |    |||    |  || | |  ||    |    ||  | ||  ||  | | |  ||| | || || |||||||||||||| ||||| ||||| || || |||||||| ||| |||||||||| || ||||| ||||| ||||||||||| || || 
gttctatgaagggaaaaattacctttccatctgttcatctgttgtataatttgtttggcatacacatgagagaaaaattacctttcataaatat----gcagctgttcctgtttctttaactatttctgtttaat--ttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------aattctgcaa-catagagaatctagatat-tattctcg-atagttttattggc-aatattaactatatgcttgtt-gacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
                                                              |||  ||    |||   |  | |  || |  ||||  | | | ||  |||    |||||  |   |   | |||| |   | ||  | | | |  |    || ||| | || ||  | |||||  |||| ||||| ||||| || || |||||||| ||| ||||||| || || ||||| ||||| ||||||||||| || |||
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------aattctgcaacataga-gaatctagatattattctcgatagttttattggcaatattaactatatgcttgttga-caagtgagtgattgtttaactttgta----gGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
                                | || |  | | |||  |||  ||| | || ||   |||   | |      ||| || | ||| ||||  || | ||  ||| | ||| | ||  | | ||    || | |||||| ||||||| || |||||||| ||||| ||||| |||||||| ||| |||||||||| |||||||| || || ||||||||||| || |||
gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0059g01220.t01 (Vitis vinifera), 3'ss of exon 5
---aattctgcaacatagagaatctagatattattctcgatagttttattggcaatattaactatatg-cttgttgacaa--gtgagtgattgttt--aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
    |   ||   | || |   |||   ||   ||   ||   | |||||   |   |||   | |   | | ||||  |  ||  || |||  ||  || |||  ||||| || ||  ||||||| || |||||||| || |||||||| |||||||| ||| |||||||||| |||||||| ||||| ||||| ||||||||||| 
gtacagcatgagtcttatatggtctttttaagcttgaagagtctcttatttatatatttagtcagagatcctcttgatgaaggtttgttatttctttaaaattttcagGGGTAAAAAGTTGAAAACACGGGTCATTGGATGTCCAAAGACCATTGATGGCGATTTGAAATGCAAAGAGGTTCCCACAAGTTTTGGCTTTGACACTGCA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 5
aattctgcaacatagagaatctagatattattctcgatagttttattggcaatat--taactatatgcttgttgacaagtgagtgat-tgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
   | |  ||   ||| |      || | ||  ||   |     | || |  | |  |||  |     ||||| |    |   |||| | | | ||     ||||| || || |||||| |||| || ||||| ||||||||||| |||||||| ||| ||||||||||||||||||| ||||| ||||| ||||| ||||| 
---tgttaaattcagaaatctactatgtgatcatcagaataagaactgactctttagtaatcagtgatttgtttaactttatttgatctatctgacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGGTGATTTGAAATGCAAGGAGGTTCCCACAAGTTTTGGATTTGATACTGCA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 5
aattctgcaacatagagaatctagatattattctcgatagttttattggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
                        ||| |||||||     ||||||   | | |  ||  |  || || |||||    ||  | |  ||      |  || |  | |||| ||||||||| ||| || || |||||||||||||||||||| ||||| ||  ||||||| || || |  || || || || ||||| || 
---------------------gttatagtattctc-----ttttat---ctagaaaaaaaaagtgttt-ttgacgttcgatcgct--ttctgtcatccagAGCAAGGAACCTGAAAACTCATGTTATCGGATGCCCAAAGACTATTGATGGTGATCTTAAGAGCAAGGAAGTGCCGATTAGTTTCGGATTCGACACAGCC

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 5
aattctgcaacatagagaatctagatattattctcgatagttttattggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
                        ||| |||||||     ||||||    || |  || | |     | ||||     ||  | |  ||      |  || |  | |||| ||||||||| ||| || || |||||||||||||||||||| ||||| ||  ||||||| || || |  || || || || ||||| || 
---------------------gttatagtattctc-----ttttatctagaaaaaaaagtgt-----ttttgatgttcgatcgct--ttctgtcatccagAGCAAGGAACCTGAAAACTCATGTTATCGGATGCCCAAAGACTATTGATGGTGATCTTAAGAGCAAGGAAGTGCCGATTAGTTTCGGATTCGACACAGCC

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|58598594|gb|CK009122.1|CK009122
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAG                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAA-GACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
EST: gi|218497540|gb|FG953486.1|FG953486
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAG                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
EST: gi|58675628|gb|CK064315.1|CK064315
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAG                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
EST: gi|5003496|gb|AU068645.1|AU068645
EST:     GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAN                         GGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG
genomic: GGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgttggcccct ... aactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT
     aatattaactatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattctgcaacatagagaatctagatattattctcgatagttttattggcaatattaactatatgcttgttgacaagtgagtgattgtttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT