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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taactactcttgatgctttaatacctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG

Basic information

species Oryza sativa
transcript LOC_Os02g04710.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 5
-taactactcttgatgctttaatacctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
  |  |  |  | ||   ||   |     |   |  || ||  |||| || |          |  ||  |        |     | |     ||| | |||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||| || || ||| ||||| | |||||| | ||| |||| |||||||
ccagtttatgctcatagattgtgaaacttttgttataagtgtacagt-atattttatttcttaacgttgttcgactgattgttgcaagaaattctgtgcagGTATTGAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 7
--------taactactcttgatgctttaatacctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
        | | | ||| | ||| |   | || |    |  || | | ||   | || ||     ||   |    |  ||| |     ||  |       || | |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||| ||||| | || ||| | ||| |||| |||||||
atgttcagttattgctcat-atgttgcgaaacttttatatatagatttcttgattatttcttaatattgttcaactgattgccgcaagaaatt-------ctgtacagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCCTTCAAACTCCACATCCCACGAGTCTATGACTACTTGTGGCTTGCTGAAGATG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0054g01550.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------taactactcttgatgctttaatacctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
                                     ||| |   ||   | || |  | |       ||  || ||     || | ||      | |||   | |||||   | | |   |||    | | | ||||| ||||||||||||   ||||||||||||||||||||||||||||| || ||  | || ||||||||| |    |||||  | |||||||| ||||| |
gtacatgtgaagtatagaaaggtcctttgaactgcaataaatgtactgattactctggtgctc--ctgatctaattgtctgttcttttc---tgttccatgaaggtcttgatttccta--ttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
--taactactcttgatgctttaat---acctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
  |   || |  |    || || |         |  ||  || ||     || | ||      | |||   | |||||  |||      |||    | | | ||||| ||||||||||||   ||||||||||||||||||||||||||||| || ||  | || ||||||||| |     ||||  | |||||||| ||||| |
cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttc---tgtttcatgaagctcttg--atttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0054g01180.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------------------------------------------------taactactc----ttgatgctttaatacctgatgaattaaactgctcagtcatgtcaggcaatac-attgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
                                                                            || || ||     | ||    |  |  |  | | | || | ||  |      |      |  | | ||   | |||||  |||      |||    | | | ||||| ||||||||||||   ||||||||||||||||||||||||||||| || ||  | || ||||||||| |    |||||  | |||||||| ||||| |
gtacatgtgaagtatagaaaggtcctttgaactgcaataaatgaactgattactattaattaagaacgaaaccagttagcttcttcaattcgaccactctactcaggttcacttgatctaattgtctgttcttttctgttccatgaagctcttg--atttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTATTGATTATTTGTGGATTGCTGAAGACG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0054g01120.t01 (Vitis vinifera), 3'ss of exon 6
--taactactcttgatgctttaat---acctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
  |   || |  |    || || |         |  ||  || ||     || | ||      | |||   | |||||  |||      |||    | | | ||||| ||||||||||||   ||||||||||||||||||||||||||||| || ||  | || ||||||||| |    |||||  | |||||||| ||||| |
cttctttagttctaccactctactcaggtgctcttgatctaattgtctgttcttttc---tgttccatgaagctcttg--atttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0054g01090.t01 (Vitis vinifera), 3'ss of exon 8
--taactactcttgatgctttaatacctgatgaa-ttaaactgctcagtcatgtcaggcaatacattgt-gttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
  |   || |  |    || || |  | | ||   || | ||  |      |      |  | | |||  | |||||  |||      |||    | | | ||||| ||||||||||||   ||||||||||||||||||||||||||||| || ||  | || ||||| ||| |    |||||  | |||||||| ||||| |
cttctttagttctaccactctact--caggtgctcttgatctaattgtctgttcttttctgttccttgaaggtcttg--atttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCCAGAATTTTTGATTATTTGTGGATTGCTGAAGACG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0054g01110.t01 (Vitis vinifera), 3'ss of exon 9
--taactactcttgatgctttaat---acctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
  |   |  |  |    || || |         |  ||  || ||     || | ||      | |||   | |||||   | | |   |||    | | | ||||| ||||||||||||   ||||||||||||||||||||||||||||| || ||  | || ||||||||| |    |||||  | |||||||| ||||| |
cttctttgattctaccactctactcaggtgctcttgatctaattgtctgttcttttc---tgttccatgaagctcttgatttccta--ttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTGATTATTTGTGGATTGCTGAAGACG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0054g01200.t01 (Vitis vinifera), 3'ss of exon 1
--taactactcttgatgctttaat---acctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
  |   || |  |    || || |         |  ||  || ||     || | ||      | |||   | |||||  |||      |||    | | | ||||| ||||||||||||   ||||||||||||||||||||||||||||| || ||  | || || |||||| |     ||||  | |||||||| ||||| |
cttctttagttctaccactctactcaggtgctcttgatctaattgtctgttcttttc---tgttccatgaagctcttg--atttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATCCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG

upper sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0054g01250.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------------------------taactactcttgatgctttaatac--ctgatgaattaaactgctc--agtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
                                                                                            |||      | | | ||||| | |  |   |  | | |  |||||    ||   |       | |||   | |||||  |||      |||    | | | ||||| ||||||||| ||   ||||||||||||||||||||||| ||||| || ||  | || ||||||||| |     ||||  | |||||||| ||||| |
gtacatgtgaagtatagaaaggtcctttgaactgcaataaatgtagtgattactaagttcaataaatgtaccgattactattaattaagaactaaaccagttagcttctttagttctaccactctactcaggtgctcttgatctaattgtctgttccatgaaggtcttg--atttcctgttatctaatttgtacagGTGTTAAATATGATTTGCTGCTGGATTGAAGATCCAAACTCGGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG

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|2310417|gb|C26572.1|C26572
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|33675594|gb|CF303833.1|CF303833
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|58690263|gb|CK078950.1|CK078950
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|29646295|gb|CB651302.1|CB651302
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|29676836|gb|CB673111.1|CB673111
EST:     ATTATGACGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
EST: gi|33675264|gb|CF303503.1|CF303503
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTC
EST: gi|29617095|gb|CB622107.1|CB622107
EST:     ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAG                         GTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC
genomic: ATTATGAAGATGAGAACACCCGATATATTTGCATTGGTCCAGTAAACAAGgtaatttgaa ... ctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
                                     tctattctctctattc  CT-rich tract
                                  aaatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taactactcttgatgctttaatacctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG