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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactttgtcaaccgaatgactaaaaagaagccatatgatgactgatacataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

Basic information

species Oryza sativa
transcript LOC_Os06g36770.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
gtgagactttgtcaaccgaatgactaaaaag-aagccatatgatgactgata----cataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
|||| | | | ||||| |||| | ||||||| |||| || ||||||   | |      |||| |     ||     | |||||| | ||||||||||| ||||| |||||||| || ||||| |||||||| |||||||||||||||||||| | ||||||||||||||| |||||
gtgaaattctctcaactgaataattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatg-------actgatacataat--ctagct-gtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
|| ||| |           || | |||  || |   |  |  ||       |   |  |||| |  || |||  |  | |  |   ||| | |||||| | ||||| || || ||||| ||||| || |||||||||||||| ||||| |||||| | | |||| |||||||||| ||  |
gttagattcccatgtttatataagtaatgagcaatgaattcctgctgctttatcaagtcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatgactgatacataatctagctgtactctaat---tttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
||||||  || |           ||   |       ||    ||  ||| |  ||| |  | | |  | ||     || ||| |||| ||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||| |    || ||||| ||||| ||  |
gtgagagcttctttctgtggcatcttttatttgttgattctgtg-ttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------gtgagactttg---tcaaccgaatgactaaaaa----gaagccatatgatgactgatacataatc--tagctgtactctaatttt---cagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
                                   ||   |||||   | ||  || | | |            | || || ||      ||  ||||   || |  || |  ||| ||   ||| | |||||| | ||||| || || || || || |||||||||||||||||||| ||||| |||||||| |  || || |||||||| ||  |
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttattttgggctttattgtcaaataatatgaactatttaattattatcattatttaaatcttgatcagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
---------------gtgagactttgtcaaccgaatgactaaaaagaagcc-atatgatgact---gatacataatct-------------------agctgtactctaatttt---cagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
                |   | | | ||| |  || | | || ||| | || |||| ||   |     |  || || |                   |  |||||||| || ||   ||||| || ||| ||||||| || || ||||| |||||||| |||||||||||||| ||||| ||||||   |  |||||||||||||||||  |
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 10
------------gtgagactttgtcaaccgaatgactaaaaagaagccat--atgatgactgataca----taatctagctgtactcta---attttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
             ||  | |  |     ||       | |   |||| |   ||  ||    |||||     |||  ||  |  || |     | | ||| | |||||| | || |||| |||||||||||||||||| |||||||| || |||||||| ||||| || |  ||||| |||||||| ||| |
ttctgttatcagctgcaattgggattgtcggtgagaaacagttaagctactaattttgttcaatacagtaacaattcagtggagctttctgtgtctgcagCTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 10
------gtgagactttgtcaaccgaatga--------ctaaaaagaagccatatgatgactga-tacataat--ctagctgtactctaa----ttttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
      || | | | | | | || | | |        | | |  ||||   |    |   |||  |  |  |  | |  | || | ||     ||| ||| | |||||||| || ||||||||||| || || ||||| |||||||||||||||||||| |||||    | ||||||||||||||| ||  |
agaaaggtcacattgtcttagccaattcaaatggtatcgacattgaagatctgcagttggtgaacatttgcttaccaattttattttataccttttacagCTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 10
------------gtgagactt-tg--tcaaccgaatgactaaaaagaagccatatgatgactgatacataatct-----agctgtactctaatttt-cagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
            ||    ||  ||  | ||    |||| ||   ||   ||  |   |      ||   ||  |     | || | | |   |||| ||| | |||||||| |||||||||||||| || || ||||| ||||| ||||||||||||||||||||  | | ||| ||||||||||| ||  |
gcttcaaataatgtatagctagtggcttaatacgatgattagtcagttacccgagtgttttctttattgaacttgtagaaactattcgcgtcttttgcagCTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
----------------------gtgagactttgtcaaccgaatgactaaaaagaagccatatg-atgactgatacataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
                      |  |||    |  ||     ||  ||       | | | || ||       ||| ||  ||  |    | |  ||| ||| | |||||||| ||||||||||| ||||| || || || |||||||||||| | ||||| |||||  | | ||| ||||||||||| ||  |
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttt--tttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 10
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatgactgatacataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
                 |  |   |  |       |   || | |||||    |   || | | |  | |   || |||||||||||  ||||||||||||| ||  |||| |||||||| ||||| ||| | ||||| ||||| |||| ||| ||||| || || ||  |
--------------gttgcgtctttcgatgtcgttcgggtggtcactgac---tttgctggttct--tttgcgttgcagTTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAG

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 10
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatgactgatacataatctagctg--tactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
                    ||  |     || | | |  |     || | | | |  | || |  |  | |   || |||||||||||  ||||||||||||| ||  |||| |||||||| ||||| ||| | ||||| ||||| |||| ||| ||||| || || ||  |
------------------gttgcgtctttcgatgtcgttcggg---tggtccctgactttgcgggttcttttgcgttgcagTTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAG

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|58655643|gb|CK044323.1|CK044323
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGG-TCGTGGA-ATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|58675521|gb|CK064208.1|CK064208
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|66913089|gb|CX099937.1|CX099937
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|58687462|gb|CK076149.1|CK076149
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|218501369|gb|FG965487.1|FG965487
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|58658882|gb|CK047562.1|CK047562
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|25807737|gb|CA763698.1|CA763698
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|88411135|gb|CI606354.1|CI606354
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|29644040|gb|CB649047.1|CB649047
EST:     TCCAGGTTCATGAACCCTTAAGGCCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: TCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
EST: gi|58688813|gb|CK077500.1|CK077500
EST:     ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGGCCAAG                         TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT
genomic: ATTCAGGTCCTGTTTCAACCTTCCAGGTTCATGAACATTTAAGGCCCAAGgtgagacttt ... taattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaagaagccatatgatgactgatacataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG
                                                ttttc  CT-rich tract
                        atacataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactttgtcaaccgaatgactaaaaagaagccatatgatgactgatacataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA