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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g03260.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 8
gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
||  | ||| ||||||  | ||  || || ||||     ||     | |  | || ||| || |  ||| | |||||||| ||||||||||| || |||||||| |||||||||||| ||||||||||||| ||||| ||||| |||||||| ||| ||||||||||||| || ||||||
gtgcgttccctgctcaagattatcttaattaattg---ccacaccacgtaacattgaacttagtccttttcacaaacttgctagATGGAAGAACGTATGACACTATGCAACATGGTTGTTGAAGCTGGTGGAAAGAACGGTGTCGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G133988_T01 (Zea mays), 3'ss of exon 2
gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
|| || | |  |||||  | ||  ||  | ||||        ||| |||  | || ||| || |  ||| |||| | ||| |||||||||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| ||| ||||||||||||| || ||||||
gtgtgtttctggctcaagattatcttagttaattgccac--acttgcataaccttgaacttagtccttttcgcatatttgctagATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 7
gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaata-tttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
|| || | |  |||||  | ||  || || ||||     ||   | |||  | || ||| || |  ||| |||| | ||| |||||||||||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| ||| ||||||||||||| || ||||||
gtgtgtttctggctcaagattatcttaattaattg---ccacactgcataaccttgaacttagtccttttcgcatatttgctagATGGAAGAGCGTATGACACTATGCAACATGGTTATTGAAGCTGGTGGAAAGAACGGTGTTGTGCCTGCTGATGAAACTACATTTAAATACCTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 9
------gtatgctccgtgctcataactagat---tgatcaattattttcatcttt-catggcttttaacctaatatttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
       ||   |     ||  |  ||   |   || |   |||||| ||    |  | | ||||| |  |  | | |         | ||||||||||||  | ||||||||||||||||||||||| |||||||| || || || ||| ||||  |||| |||  ||| ||||  || || ||||||
gtatgcatacttttaacactgttttctttctatatggtatgttatttgcactagtataagacttttgaattgttgtatt-----gtattgtagATGGAAGAAAGGATGACACTGTGCAACATGGTTATAGAAGCTGGAGGGAAAAACGGTATTGTTGCTGCTGATAGAACCACATACAAATACCTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 8
------------------gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttgg-tagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
                    ||      | ||   ||    |    ||  |  |||| ||  |  ||     ||    |  || ||       ||||| ||||||||||| || |||||| |||||||||||||| ||||||||||||| |||||||||||||| ||||| ||    ||||||||||| |||||||| 
aaaacacaagtaaacgggccataaatttttctt-caatctcagaactctttcttttttattataaataaaagttgttttggtaatttgttcctcttggataGATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGA-

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 8
--------------gtatgctccgtgctcataactagatt--gatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttgg-tagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
                  || |     |  |    |   |  || |  ||  |||    | | |      ||    |  || ||       ||||| ||||||||||| || |||||| |||||||||||||| ||||||||||||| |||||||||||||| ||||| ||    ||||||||||| |||||||||
gaaaacacaagtaaacgggccctaaatttttcttcaatctcggaactctttcttttgattataaataaaattgttttggtaatttgttcctcttggatagATGGAAGAACGGATGACATTGTGCAACATGGTTGTTGAAGCTGGTGGAAAGAATGGTGTTGTTCCTGCTGACAGCACTACATTTAAATATCTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------gtatgctccgtg-ctcataactagattgatcaattattttcatctttcatggcttttaaccta---atatttccgcaaactt---------ggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
                              |  |  || |  || |||   | |   || ||| |  | ||| |    |     || |  ||   ||  || |   ||  |         | |||||||||||  |||||||| |||||||||||||| | |||||||| || |||||||||||  | ||| | |||   || ||||| || ||| |||||
gtaagaaatcattctatatttcctacattatgggtcccttctcttatagaaataaaaattaat-agctgcatatgatgttatcattgatttataaatggttgcttgaatcttttttggctgctagATGGAAGAAAGAATGACATTGTGCAACATGGTTGTGGAAGCTGGGGGAAAGAATGGTGTCATCCCTCCTGATGCGACGACATTAAATTATGTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------------------gtatgctccgtgctcataactagattgatcaattattttcatctt--tcatggcttttaacctaatatttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
                                           |   | | |     |    |  ||| | ||| |   |  |||   |||  | ||| |   |   |||     |||||    ||||||||||  |||||||| | ||||||||||||||||||||||| || |||||||||||||| ||||| |||   ||||||  ||| || ||||||
gtaggtgcacttttatagatcttccactgcaagtatctaaatcactgttcatttctgtgtggaatttgtttaatcagcctgttctggatcacagttttgattgtttcattgttctaaactgaaaagATGGAAGAAAGAATGACATTATGCAACATGGTTATTGAAGCTGGGGGAAAGAATGGTGTTGTCCCTGCTGATAGTACTACACATAAGTACCTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------gtatgctccgtgctcataactaga--ttgatcaattattttcatctt--tcatggcttttaacctaatatttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
                                              || |   |  |  ||  |  |||   ||| |   |   ||   | |||| ||| |   |  |||| |    ||||    ||||||||||  | |||||| | |||||||||||| |||||||||| || |||||||||||||| ||||| |||   ||||||  ||| || ||||||
gtaagttcacttttacagatcttcccctgcaaaaatctcaagtcattctgcatttctttctgaaatttgtataatcaaactgcactggattatggttttaattgttttattcctctcaactgaaaagATGGAAGAAAGGATGACATTATGCAACATGGTTGTTGAAGCTGGAGGAAAGAATGGTGTTGTTCCTGCTGATAGTACTACACATAAGTACCTTGAG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 8
--------gtatgctccgtgct--cataactagattgatcaattattttc-----atctttcatggcttttaacctaatatttccgcaaacttg--gtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG----
        |  |  | ||| ||  |   |||  |   |    ||||||||        |     | ||||    ||  |   |  | ||| |    ||||||||||||  ||||||| ||||||||||||||  | |||||||| ||||||||||| ||||| ||||| |||   || ||    || ||  | ||     
aatcgttggctttattcgtactttctcgactgcacgaagagtttattttctagaggcttgctgggtctttctgactgctgcatttggaaattacatgtagATGGAAGACAGAATGACTCTGTGCAACATGGTCGTGGAAGCTGGAGGCAAGAATGGCGTTGTTCCTGCTGATGCCACAACCGCGAAGTACTTGGAAGGAA

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 7
gtatgctccgtgctcataactagattgatcaattattttcatctt-tcatggcttttaacctaatattt---ccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
                     ||  |  |   ||    | | ||  ||  |  | |  |||| || |      || ||     | ||||||| ||  |||||||  ||||||| ||||  ||||||||||| ||||| ||||| ||||||||||| ||| ||   || | ||  |||||  ||
------------------gtcag--tatttttttccccttacctcatcgagattgtccacctgatttcgagatcggaactcacgcagATGGAGGACAGAATGACGTTGTGCAATATGGCGATTGAAGCTGGAGGCAAAAATGGCGTTGTGCCTGCGGATGAAGTCACCTATAGTTATCTGAAG

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG
                        ttttaacctaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctccgtgctcataactagattgatcaattattttcatctttcatggcttttaacctaatatttccgcaaacttggtagATGGAAGAGCGAATGACACTGTGCAACATGGTTATTGAAGCTGGTGGCAAGAATGGTGTTGTGCCTGCCGATCAAACTACATTTAACTATCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA