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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA

Basic information

species Oryza sativa
transcript LOC_Os09g04110.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G010054_T01 (Zea mays), 3'ss of exon 1
tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgggatatggaa---ttgttgaatcgtagattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
 | ||  | ||||  |    |     | | |  | ||   ||| ||||  |  || ||   ||  | |      | || |  | || |||| ||    ||||||||||||||| ||||||||||| |||||||||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| ||||||||||| ||
aggtctacttggtacttgcacaacagtcggtaagagc-gttaccattgttacttgtaaaacttactaatattctggtttt--gcttactgtcatatgatgcagGTGATGATTATAAGATTAAGGTCTGGAATTACAAGACACACCGTTGCCTTTTCACACTTCACGGACACCTTGACTACATTCGCACTGTGCAATTCCATCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 1
tgttccgcctggttgtatttctgggatagctgtgggc-taatacgattggga--tatggaattgttgaatcgt---agattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
   |||   |  |  |    ||   | | |  | |||  | ||| ||||  |  | |   |||  |||||| |   |||||||   |   ||||  | |  ||||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||
-aatcca--tactaatgcaactaatacatccttcggcacattacaattgttacttttaagatttatgaatcttctaagattctggta---ctgttttaccatgcagGTGATGATTATAAGATTAAGGTCTGGAATTACAAGACGCACCGCTGCCTCTTCACACTTCATGGGCATCTTGACTACATTCGCACCGTGCAATTCCATCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G33270.1 (Glycine max), 3'ss of exon 1
tgttccgcctggttgtatttctgggatagct-gtgggctaatac----gattgggatatggaattgttgaatcgtagattc--taagatttctgtgatgca--ttgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
              |||  ||     || ||      |   |||    |||  | ||||    |      |||  |   ||  |||   |  | | ||       |||||||| |||||||| || ||||||||||| ||||||   ||||||||||||||||| || |  || ||||| |||||||| ||||||||||| ||||||||
--------------gtaactcgtaactaactcaccatccgttaccctagatctgcatataatttccccagatccgaacctcgctaaccctaatctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACGCTCCTCGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G34310.1 (Glycine max), 3'ss of exon 1
tgttccgcctggttgtatttctggg-atagctgtgggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
           ||   |  | |    | | ||       | | |   |  |||  | |  |    || |  |   |||||    |||    |     |||||||| |||||||| || ||||||||||| ||||||   ||||||||||||||||| || |  || ||||| |||||||| ||||||||||| ||||||||
-----------gtaacaaatttaactagatctacatatcatttc--ctcagatccgaaccttgctaaccccaa--tctaa----tctaatctcacccgcagGTGACGATTACAAAATCAAGGTGTGGAACTACAAGCTCCACCGCTGCCTCTTCACCCTCCTGGGCCACCTCGACTACATCCGCACCGTGCAGTTCCACCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 2
---tgttccgcctggttgtatttctgggatagctgtg--ggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtgatg-cattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
   | |       ||    |||  | |   |   ||    ||| | | || ||| || |  |  || |   | | |  | | | ||| |   |  ||  |||||||| ||||||||||||||||| |||||||| ||||| |  ||| | ||||| ||||| ||||  ||||| ||||| || || ||||| || || ||||| ||
gtatatataattcggaatcattgttagtgaaatcgtataagctcaaaagaatgg-atctatacatgatttgttgcat-tacaatgatgttgatcttgatattgcagGGGATGATTACAAGATTAAAGTGTGGAACTACAAAAACCACAGGTGCCTTTTCACTCTTCTAGGGCATCTTGATTATATCCGCACGGTTCAGTTCCATCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
-----tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
           || ||| |   | |  |  | || |      |||| |  ||     |    | |  |   | || |||   |    ||   |      ||||||| ||||||||||||||||| || ||||| ||||| || ||| | || || ||||| ||||  ||||| ||||| || || ||||| || ||||| |||||
aaatgcaaatggcttggattcttcttcgttacagtta-----taatgctcttacagaacattactcatatgtagttgatggcattgattacattggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 2
--tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtgatgcattg-cagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
    ||      || || |    |  ||||    |    |  |  |  || |      |||| |||  |  |  |    | | ||| |  | |   ||  |||| |||||||||||||| |||||||||||||| |||  |||  | ||  | || || |||  ||| |||||||| ||||| ||||| || || || |||||
ggaattttatggggctggacccataagata---atatatttgtgtgcctgtgtgtatcaatttttggtttatgcaaatgatggttttttggttattttttcagGAGATGATTACAAGATCAAGGTGTGGAATTATAAGTTACATAGGTGTTTATTTACCCTTTTTGGACACCTTGATTACATCCGCACAGTTCAGTTTCACCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
-tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtga--tgcat--tgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
 | ||  |||||||| || ||   ||    |  | || |  |  |||      || | |    |      || | | ||| |  | |  ||  ||||   |||||| |||||||||||||| ||||| ||||| |||||||  |  || || || |||||  |    || ||||| || ||||| || || || |||||||| ||
ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctat-----ataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S11_79V6.1 (Physcomitrella patens), 3'ss of exon 1
tgttccgcctggttgtatttctgggatagc-tgtgggcta---atacgattgggatatggaattgttgaatcgtagattctaagatttctgtgat--gcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
      |  |      || |    ||||   ||| |  |     | ||||    |  |    |   | |||  |    |||| |  ||  |  |   | | || ||| ||||| ||||||||||||||||||||||||||||  |  |||||  | || ||  |    || ||  | ||||| || || || ||||||||||||||
------gattacccacatattgaagatattatgtagattttgtgtgcgatgcccacttaatttgtattaatattgtgctctacgtgtttgggaaccgggaatgtagGGGATGACTACAAGATTAAGGTGTGGAATTACAAGATGCGGCGCTGTTTGTTTACTTTGTTGGGTCATTTGGACTATATCCGGACGGTGCAATTCCACCA

upper sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ32142 (Selaginella moellendorffii), 3'ss of exon 1
--tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgg--gatatg---gaattgttgaatcgtagattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
         ||| | | |  |    |       |     |  | |||| |   ||| |    |  ||  ||| |||  | |   | |||  ||    |   ||  ||||||||| |||||||| ||||||||||| ||||||||     | ||||| ||||| || |  || ||  | || ||||| || || || || ||||| ||
gtaagatttccttgctttcctcaccgatcgatcgacattttgttcgatcgaccgatttctttgctttcctgagtcgctgctgaaaggatccct----tctttttaagGTGATGACTACAAGATCAAGGTGTGGAACTACAAGACGAGGAGATGCCTGTTCACGCTGCTGGGCCATTTGGATTACATCCGGACAGTCCAGTTCCATCA

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|29621302|gb|CB626313.1|CB626313
EST:     CGTCCGCGGCGTCCACTTCCACGCCACCCAGCCGCTCTTCGTCTCCGGAG                         GTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCT
genomic: CGTCCGCGGCGTCCACTTCCACGCCACCCAGCCGCTCTTCGTCTCCGGAGgtcagtcaat ... tgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggatatggaattgttgaatcgtagattctaagatttctgtgatgcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA
                               taagattt  TA-rich tract