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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtag

Basic information

species Oryza sativa
transcript LOC_Os02g03260.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G370852_T03 (Zea mays), 5'ss of exon 8
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtag
||||||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||  ||  | ||| ||||||  | ||  || || ||||     ||     | |  | || ||| || |  ||| | |||||||| |||
ATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgcgttccctgctcaagattatcttaattaattgc---cacaccacgtaacattgaacttagtccttttcacaaacttgctag

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G133988_T01 (Zea mays), 5'ss of exon 2
----------------------ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtag
                      ||||||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||  || || | |  |||||  | ||  ||  | ||||        ||| |||  | || ||| || |  ||| |||| | ||| |||
TCTTGTTAATTGCTACTTACAGATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCAATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgtgtttctggctcaagattatcttagttaattgccaca--cttgcataaccttgaacttagtccttttcgcatatttgctag

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G010044_T02 (Zea mays), 5'ss of exon 7
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtag
|||||||| |||||||| |||||||| || || |||||||| ||||||||||||||||||||||| ||||||||||  || || | |  |||||  | ||  || || ||||     ||   | |||  | || ||| || |  ||| |||| | ||| |||
ATTATTGGAGAGATTTCAGTATCTGGTGCGACCTACAAATCAATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACCgtgtgtttctggctcaagattatcttaattaattgc---cacactgcataaccttgaacttagtccttttcgcatatttgctag

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 8
-ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattatttt-catctttcatggcttttaacctaatatttccgcaaacttggtag---------------------
 ||||||||||| ||  ||||  |||| |||||||| ||||| ||||||||||| ||  ||||||| |||||| ||| |||| |     |   || | | |||| | |  |||||  |  | ||   |  || | |   ||  ||||| |     ||   |                       
GATTATTGGTGAAATAACTGTGGCTGGTGCAACATATAAATCGATGGAGTTTGTCGGTACAACTGTTGAAAGTTTAACtgtaag-----tatgcacagcaagat-gttatattatgatgtaactccaagtgcctgtttacttgtattttctttttctgttttcattttttgttttctcttttta

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA14G40570.1 (Glycine max), 5'ss of exon 8
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgc-tccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtag-----------------
||||||||||| ||  ||||  |||| |||||||| ||||| ||||||||||||||  |||| || |||||| ||| |||| |  | |      |||  |    | || |  ||  | ||  |  |  |  ||||    |  | ||| | |    |   ||                  
ATTATTGGTGAAATAACTGTGGCTGGGGCAACATATAAATCGATGGAGTTTGTTGGTACAACCGTTGAAAGTTTAACTgtaagtatgcacagcaatattttatattatgatgtaactccaagtgcc-cgtattttcttttcctgttttcactttttaattacaaaattgccatcttgtt

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G34160.1 (Glycine max), 5'ss of exon 9
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtag----------
|| |||||||| || ||||| ||||| |||||||| ||| | ||||||||||||||  ||||  | |||||| ||| |||||||    | ||  ||||    ||  ||  |   | |  | | | ||      ||   ||| | ||  | ||   | |||           
ATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGTgtatgc---atacttttaacactgttt-tctttctatatggtatgttatttgcactagtataagacttttg-aattgttgtattgtattgtag

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 8
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgat-caattattttcatctttcatggctttta-acctaatat-ttccgcaaacttggtag-----------------------------------------
||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||  | ||||| |||||| ||| |||| | | |    | |||  |       | ||| ||| |  |||  |  |   || |      ||| | ||     | | || |                                           
ATTATTGGTGAAATATCTGTTTCTGGCGCGACATATAAATCTATGGAATTTGTTGGCACTACTGTTGAAAGTTTAACTgta-ggtgcacttttatagatcttccactgcaagtatctaaatcactgttcatttctgtgtggaatttgtttaatcagcctgttctggatcacagttttgattgtttcattgttctaaactgaaaag

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 5'ss of exon 8
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtag--------------------------------------------
||||||||||| || || || ||||| |||||||| ||||||||||| ||||||||    ||||| |||||||| | |||| | ||  |  |    |          |||  || |  |    |  ||  |||    || | ||||    || |    |                                              
ATTATTGGTGAAATATCAGTTTCTGGGGCAACATATAAATCCATGGAATTTGTTGGCAGTACTGTTGAAAGTCTGACTgtaagttcacttttacagatcttcccctgcaaaaatctcaagtcattctgcatttctttctgaaatttgtataatcaaactgcactggattatggttttaattgttttattcctctcaactgaaaag

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ16666 (Selaginella moellendorffii), 5'ss of exon 7
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtag
|| ||||| |||||  |||| || || |||||||||||||| ||||||||||||||| || |||| ||| || | |  ||  |     |  ||    ||    | ||| |   | | || ||     |  ||  |       | |  ||||          
ATCATTGGAGAGATCACTGTTTCCGGTGCAACATACAAATCAATGGAGTTTGTTGGAACAGCTGTAGAACGTATGACGgtcagtatttttttccc--cttacctcatcgagattgtccacct-----gatttcgagatcggaactcacgcag---------

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|88340371|gb|CI659577.1|CI659577
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|218494441|gb|FG968569.1|FG968569
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|88336267|gb|CI648854.1|CI648854
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|88307301|gb|CI641939.1|CI641939
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|2312204|gb|C28359.1|C28359
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATNACACTGTGCAACATGGTTATTGAAGCTGGTNGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|88329810|gb|CI651478.1|CI651478
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|88571723|gb|CI663096.1|CI663096
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|88326072|gb|CI651125.1|CI651125
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|218490400|gb|FG966882.1|FG966882
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
EST: gi|29628818|gb|CB633829.1|CB633829
EST:     CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT                         ATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG
genomic: CAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccg ... aacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAATgtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtag

- - - - - - - - - - - - - - - - - - - -  CATGGA