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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G141725_T01 (Zea mays), 3'ss of exon 3
aactaatgttctatttccttgtcacgactattatgttggattcaatg------gtacatttggt-ctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGA--GTGGG-ATGAAGTGGAGAAATATCTTTCAGGTTTC--
     || || ||  || ||   |   |  | ||||| | | |||||       |  |||     || | || |   |     ||||||    |    |  ||  |||  |  ||  | |   ||  |    |  |    ||| |||||   ||       | | |  |  ||   | || ||    || |||  | ||||| || || |  
-----attttttaagtcattaaaagtgcc-tcatgtttggtgcaatgcaattaatgtattcttcactggtaatgaaaataggactaatagatcatgaaccatta-agGTCTACGCTGGGGAGTGGGATGAGGTGGA----GAAATACTTGTCAGGTTTCACCAAGGTAGACGACAATAGGTATTCGATGAAGATCT-TCTTTGAGATTACCA

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G477539_T01 (Zea mays), 3'ss of exon 3
aactaatgttctatttccttgtcacgactattatgttggat-tcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC------
 | |  | ||  |  | |||    |  | ||| | |  |   | ||   | |||   || | |     || ||||    |||   |||  |||         || |      |   ||||  ||  |  | ||||||  | |        |||||| | ||||||||||||||||| |||||||||||  | |||||||||      
-att--tcttacagcttcttactccctcgattttttaagtcattaaaaatgcatcatgtttggtgcaatgcaatt----aat---gtatcttc--------actggtaatgaaaatagGA--CTAATAGATCATGAACCATT--------AAGGTCTACGCTGGGGAGTGGGATGAGGTGGAGAAATACTTGTCAGGTTTCACCAAG

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
|||| ||||| ||   | || |     |    |  | | |||   ||     |    |    | |  ||||||       ||    ||||| |||| ||||||||||||||||||||| ||||||||||| ||||||||||| || ||||||||||||||||||||||||||||| ||||||| |||  | ||||| |||
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G116506_T01 (Zea mays), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatt--tggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
 ||| |||||||    | || |    |         ||||   |   || | ||  |  ||||  |   |||| |       ||    ||||| |||| |||| ||||||||||||| || ||||||||||| |||||||||||||||| ||||| |||||||||||| |||||||| |||||||||||  | |||||||||
-actgatgttctcccacgttctttt-atcccagaaatggaactatctgtgcgttgatattctactataatgtagtaattccctacttcacattgtgttgtagGTTTGAGCAAGAGTCGGGGTTCTTCTTCAATATGAAGTACTTTGAAGCGAAGGGCCATGCTGGGGACTGGGATGAGGTGGAGAAATACTTGTCAGGTTTC

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G442087_T01 (Zea mays), 3'ss of exon 2
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtc--tagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC--------------------
                                              | |   ||  |||  ||  || |  | || |  |  |    | || |   | |    ||| |     | | |  ||    ||   | || | | ||  | |     ||||||| ||||| ||||||||||| |||||||||||  | |||||||||                    
----------------------------------------------gattttttaagtcattaaaaatgcctcatgtt-tggtgcaatgcaattaatgt--atcttcactggtaatgaaaataggactaatagatcatgaaccatta-----agGTCCACGCTGGTGAGTGGGATGAGGTGGAGAAATACTTGTCAGGTTTCACCAAGGTAGATGACAATAG

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaag-gtgtaatttcctaatatggtacattctgttt-tagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
   ||  |       ||   |  | |     || |  |  ||  ||    |||    || |       ||| | |   | | ||| | | |  ||| |  ||||||||| |||| || || ||||| || ||||||||||||||||| || || || || ||||| |||||||| || || ||||| ||  | ||||| || 
gcatagcgaagagcctctgggcaatgg--ggtacgaagttttttatatggcatccactcgactgttcatgtcactcttttaaatgcttcttaatgtgtgcagGCTTGAGAAAGAATCTGGGTTCTTTTTTAACATGAAGTACTTTGAGGAAAAAGTGCAGGCTGGCGAGTGGGAAGAGGTTGAGAAGTACTTATCAGGATTT

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 1
aactaatgttctatt-tccttgtcacgactattatgttggattcaatggta--catttggtctagcaaggtgtaatttcctaatatggtacattctgttt-tagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
  ||  |  | ||   |  || | |  |  | | |     |||  |||| |  || | |      ||   ||| | |   | | ||| | | |  ||| |  ||||||||| |||| || || ||||| |||||||||||||||||||| || || || || ||||| |||||||| || || ||||| ||  | ||||| || 
-tctggttatttagggttttttttataaagaattttcattattatatggcatccactcgactgttca---tgtcactcttttaaatgcttcttaatgtgtgcagGCTTGAGAAAGAATCTGGGTTCTTTTTCAACATGAAGTACTTTGAGGAAAAAGTGCAGGCTGGCGAGTGGGAAGAGGTTGAGAAGTACTTATCAGGATTT

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
--aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
   |  | | ||    ||||||     |   |  || |   |||   |     || |   ||    |  | |  ||    || ||| | | ||||| |  ||||||||| |||| || || || |||||||| |||||||||||||| || || || || ||||| || ||||| ||||| ||||| ||  |  |||| || 
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgctta--tttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
      |  |||||||   ||    |  | || |||||  ||   ||  |   |   | | |  |        ||  |||| || || ||       |||||||||| |||||||||||||||||||||| |  ||||| ||||| ||||| || |  ||||| || |||||||| || ||||  ||| | |||||||| 
----gttagtctatttatatggtttg--ttttgtgttgtgtt--gtgagaggctgaattttgggattgactgatttgtaatttgttaaata------tagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
      |    |  | | |||||     | |  || | | ||   |  |     |  | | |   ||| ||||||    |  ||||  ||     | |||||| |||||||| || || |||||||| ||||| ||||||||||||||||| |  | |||||| |||||||||||||||||||| |||||||| ||||||
-----gtaagtttgtgctttgtcgtttttgt-gtgcttgtttggtttctctgcgtaattttg---ggtataatttg--gaattggttgatg----tgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 1
-aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
    |  | || | ||   ||   |     | | | |||||     ||||  | ||  |  | |    | | |      | |||  |    | | || |||||||||| |||||||||| || |||||||| |||||||||||||| ||||| || || || || || ||||||||||| ||||| ||| | || || |  
tttttttttttttcttcttttccaatttacactttcttggaagtt-tggtgtagttaattaatcttaatttgaacggaaattattttttggtgttttgtagGCTTGAGAAAGAGTCAGGGTTTTTCTTCAATATGAAGTACTTTGAGGAGAAAGTACAGGCAGGAGAATGGGATGAAGTTGAGAAGTATTTATCCGGATAT

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttgg--attcaatggtacatttggtctagcaaggtgtaatttcc--taatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
       |||   |     ||     | | | |   ||   || ||   ||   |||  ||| ||||  |||| |  |   |  |||  ||| ||||     ||| | |||||||| ||||||||||||||||| |||||||||||||||||  | || || | ||| |||||||| || |||||   |||| | || || |||
--tctgcgttacgtgaagctggtgtcattttcaaaatgtgcatacagacgtttgtttcttct-gcaatctgtactgactggttttataataccttctaacc-agGTTGGAGCAAGAATCAGGATTCTTCTTCAATATGAAGTACTTTGAAGACCAAGTTCAAGGTGGTGAGTGGGAGGAGGTGGAACGATATTTATCTGGGTTC

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
                                 ||      |   ||||   ||     | |   | |||||        | | ||    | | |   ||||| |||||||| || || |||| ||||||||||||||||||||||||  |||||||   |||||||||||| || |||||||  ||  | || || |||
--------------------------------gtgagaagatttgtggtttgttcttgttggtg-gatgtaa-------gtgttgtgtgattt-tggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
                                 ||  |   |   ||||  |||     | |   | |||||        | | ||    | | |   ||||| |||||||| || || ||||||||||||||||||||| |||||||  |||||||   |||||||||||| || |||||||  ||  | || || |||
--------------------------------gtgaggagatttgtggtttattcttgttggtg-gatgtaa-------gtgttgtgtgattt-tggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
                                 ||  |   |   ||||   ||     | |   | ||||| |     || ||    ||| ||    ||||| |||||||| || || ||||||||||||||||||||| |||||||  |||||||   |||||||||||| || |||||||  ||  | || || |||
--------------------------------gtgaggagatttgtggtttgttcttgttggtg-gatgtaagtgtt--atgtg----attttgg--cagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

upper sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 1
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
                                 ||      |   ||||   ||     | |   | |||||        | | || |  | | |   ||||| |||||||| || || |||| ||||||||||||||||||||||||  |||||||   |||||||||||| || |||||||  ||  | || || |||
--------------------------------gtgagaagatttgtggtttgttcttgttggtg-gatgtaa-------gtgttgtgcgattt-tggcagGCTGGAGCAAGAATCTGGCTTCTACTTCAACATGAAGTACTTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC

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|88431201|gb|CI574372.1|CI574372
EST:     CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAA                         GCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA
genomic: CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAAgtgcgtagcc ... tctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA
EST: gi|29637676|gb|CB642685.1|CB642685
EST:     CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAA                         GCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA
genomic: CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAAgtgcgtagcc ... tctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA
EST: gi|29625564|gb|CB630575.1|CB630575
EST:     CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAA                         GCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA
genomic: CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAAgtgcgtagcc ... tctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA
EST: gi|88386229|gb|CI572846.1|CI572846
EST:     CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAA                         GCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA
genomic: CTCATCCTCCAGTTCCTCGACGAGGAGAAGTTCAAGGAGACCGTGCACAAgtgcgtagcc ... tctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
                             tcctaat  putative branch site (score: 2)
                                            ttctgtttt  putative PPT
                        taatttcctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - -tatgttg
- - - - - - - - - - - - - - - - - - - - - - - - -acatttg