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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG

Basic information

species Oryza sativa
transcript LOC_Os12g41860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G003509_T01 (Zea mays), 3'ss of exon 3
gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
      |  ||  ||||   |   |    ||| |||    |   || |            ||  |||   | ||  || || | |||||| |||||||||||||||||||| ||||| ||||||||||| |||||||| |||||||||||| | |||||||| |||||||||||||||
----gtaataagtctggaacacggttgcatttcgtt--ttcaaactct------------atgcctgctctaatgctagtttcccagTCTACTCGCTATTGCTGAGGAGACATTGGCGGAGTTCATGTCCAAGGCGACCGGAACTGCTGTCAACTGGGTGCAGATGGTTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
|||  |   |||||||||    ||||     || |         | ||  ||||      |||          ||   ||||  |||||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||| | ||||||||||||||||||||||||
gtaagcctgaaacctggttacatttcaaaccttat---------ccttgctgtaatgctaatt----------ttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 3
-------gtatc-cacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgatt--ttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
         ||  || || |       || ||  || || | ||         | ||||    | || | | |    ||  ||  || ||    |||||||||||| || |||||||||||| ||||||||||| | || ||||| || |||||||||||||| ||||| || ||| |||||||||||
gtaagtaacattacataacataacacgtacttctttattatttttcatttcaatgttttcatggtaataataccatcattgttcatttttgtttcagTCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 3
gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgt--atgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
                    | |  || | ||    |  |     | |||  |  ||  | | |   | |      ||||||    ||||||||| || |||||| |||||||| |||| | |||| | || || || || |||||||||||| | ||||| |||||| |||||||||||
-----------------gtaagtaactccattatgcaaacaaaattgtttaattaatatatgctcattcaccattctttattctgccagTCTTCTTGCAATTGCTCAGGAGACCCTGGCGGCGTTCCTTTCAAAAGCTACTGGAACTGCTGTCAACTGGGTCCAAATGATTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 3
----gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgt-atgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
    ||| |  ||  |      | | ||| ||   ||  ||     |  ||     | || |  | |  || |      ||||||    ||||||||| ||||||||| |||||||| | |  |||||| | || || || || |||||||||||| | ||||| || ||| |||||||||||
gtaagtaacttcattatgcaaacaaatttgtttaattaatatatactcattcaccatcattacgggtctctaattc---tttattctgccagTCTTCTTGCTATTGCTCAGGAGACCCTAGTGGAGTTCCTTTCCAAAGCTACTGGAACTGCTGTCAACTGGGTCCAGATGATTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 3
-------------------gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
                     ||    | | ||      | |   |  |||  | ||    |  |  |    || || |||||    ||| ||||  ||    |||||||||||| || |||||||||||| ||||||||||| | || ||||| || |||||||||||||| ||||| || ||| |||||||||||
taacaaaaactaacaattaacatttgtagatccaaa--aaataaatattttcatcagtaaatagtaata-acat-aaggattgt--ggattatttgtttgtttcagTCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgatt-ttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
      |      || ||||  | | |   | | | | |   |   |||     |    ||   |  | ||| || || ||||   || || ||  |||| || |||||| || | ||||||||| | || ||||| |||||||||||||| || ||||| || ||| |||||||||||
---gtgagcttttcttgtctgctctataactctctaatgaattctgtttcccactctgtgacaacctaaatggttcttttttgtttagACTCCTTTCTATAGCAGAGGAGGCCCTAGCAGAGTTCCTTTCCAAGGCTACAGGAACTGCTGTTGACTGGGTTCAGATGATTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgatt-ttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
        ||     | ||| ||||  | | |   |    | |  |    | ||||| |     || |   || | || |||  | ||||||||| | ||||| |||||||||||||| |||||| | |  ||||| ||||||||||||||||| ||||| || ||| |||||||||||
------gtaaggaaggctctttttttgtttgtgaatttctcattgtgacat-tatgagaagagactaaatggagtgtttttttggtagTCTTCTCTCGATTGCGGAGGAGACCTTGGCGGAGTTCCTTTGCAAGGCTACAGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 3
gtatcc-acaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagat-tgctgagatgattttatttgcgc-----agTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
||| |  ||         | || | |  | |   |  |   | |  |||  ||  |||   |  |||| |   |  ||  |||| |      ||||| ||||| || |||||||||||| ||||||||||| |||| ||||| || |||||||||||||| ||||| || ||| |||||||||||
gtaacttactttcaactatttaatctgatataaagaaaatacctaatttcctggttgatttacatgcttacgagccttcttttgtgtgtcatagTCTACTCGCAATAGCTGAGGAGACCCTGGCAGAGTTCCTGTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

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|58656953|gb|CK045633.1|CK045633
EST:     AACCCAGCAGG                         TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGAC
genomic: AACCCAGCAGGgtatccacaa ... atttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGAC
EST: gi|58675209|gb|CK063896.1|CK063896
EST:     CAAAACCCAGCAGTTCTGCATCCGCAAAGGGATGCGAACAACCCAGCAGG                         TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGAC
genomic: CAAAACCCAGCAGTTCTGCATCCGCAAAGGGATGCGAACAACCCAGCAGGgtatccacaa ... atttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGAC
EST: gi|58609674|gb|CK037707.1|CK037707
EST:     CAAAACCCAGCAGTTCTGCATCCGCAAAGGGATGCGAACAACCCAGCAGG                         TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGAC
genomic: CAAAACCCAGCAGTTCTGCATCCGCAAAGGGATGCGAACAACCCAGCAGGgtatccacaa ... atttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 70 (downstream exon)
Score: 5

CAGATACAAGCTGTGAGTCTGTGGTGACAAGTGGTCAGCACCATCAACAGCAAAACCCAGCAGTTCTGCATCCGCAAAGGGATGCGAACAACCCAGCAGGgtatccacaa ... atttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaggccgtgcttttttgtatgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG
                                         ttttattt  CT-rich tract
             ttttttgtatgaaa  TA-rich tract