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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggataaatctgaacttcttttctcctttatttgggagttctatggcttttatagtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA

Basic information

species Oryza sativa
transcript LOC_Os10g34710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 3
gtaaggataaatctgaacttcttttctcctttatttgggagttctatggcttttatagtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
||||| |   || ||||||| || | |  | |       | ||  ||||||||  || ||||| | ||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||| |||| |||||||| ||||||||||||||||||||||||||| ||| |||||
gtaagaagtgatgtgaactttttattttttatggaattcaatta-atggctttattattgatatt-tatcgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCTGTCAATCCTTTCAAGAAAGTTTCTCTGTATGGTAACGAGTACATTGATGCATATAGAAATAAATCAATGGATA

upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 3
gtaaggataaatctgaacttcttttctcctttatttgggagttctatggcttttatagtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
||||| |   || | ||||| ||||    || | ||      |  ||||||||  || ||||| | ||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||| | || |||||||| |||||||| |||||||||||||||||| ||| |||||
gtaagaagtgatgtaaacttttttt----ttgagttcaa---ttaatggctttattattgatatt-tatcgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCTGTCAATCCTTTCAAGAAAGTTTCACTGTATGGTAACGAGTACATCGATGCATATAGAAATAAATCAATGGATA

upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 4
gtaaggataaat----ctgaacttcttttctcc---tttatttgggagttcta-tggcttttatagtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
|||||  |  ||    || || || || ||| |   ||| |||   | |  ||    |||| ||      ||| ||||  | |  |||| ||||| || || |||||||| || || ||||| ||||||||||||||||| ||||||||||| |||||||| || || |    |||| |||  || |
gtaagtctttatatcgcttaagtttttctcttcaaatttgtttcctaatcataacatctttaattacataactgtatt-caattcagACAAAAGCTGGGCCTGTTTTGGTTGCTGTAAATCCATTTAAGAAAGTTCCTCTGTATGGTAATGACTACATTGAAGCCTACAAGTGTAAATCAATTGAAA

upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 4
--------------gtaaggataaatctgaacttct-tttctcctttatttgggagttctatggcttttata-gtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
               |    | |||| |   | ||  ||| |   ||  |    | |||||  |  |||||  ||   ||||| |   | |  |||| |||||||| || |||||||| ||  | ||||| ||||||||||||||||||||||||||||| || ||||| || || |    |||| |||  || |
gtaagtctttatgtctctttaaaaattttctcatcaatttgtttcttgatcataacttctaatgtatttatgtgtataactatgt-acaattcagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA

upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 2
gtaaggataaat------ctgaacttcttttc---------tcctttatttgggagttctatggcttttata-gtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
|||||  |  ||       | || || || ||         |   ||  |    | ||  |  |  |||||  ||   ||||| |   | |  |||| |||||||| || |||||||| ||  | ||||| ||||||||||||||||||||||||||||| || ||||| || || |    |||| |||  || |
gtaagtctttatgtctctttaaagtttttctcatcaattagtttcttgatcataactttgaatgtatttatgtgtataactatgt-acaattcagACAAAAGCAGGGCCTGTTTTGGTTGCTATAAATCCCTTTAAGAAAGTTCCTCTATATGGTAATGATTATATTGAAGCCTACAAGCGTAAAGCAATTGAAA

upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 3
gtaaggataaatctgaacttcttttctcctttatttgggagttctatggctt--ttatagtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
       ||| |||  |  ||  ||    |||  |    | || | |  | |  | |||   ||||| | ||  | |  |||| ||||| || || |||||||| || || ||||| ||||||||||||||||| ||||| ||||| |||||||| || || |    |||| |||  || |
------gtaagtctttatatcactttagtttttctcttaaattttgtttcctaatcataac-atactgtgtt-caattcagACGAAAGCTGGGCCTGTTTTGGTTGCTGTAAATCCCTTTAAGAAAGTTCCTCTGTATGGCAATGACTACATTGAAGCCTACAAGTGTAAATCAATTGAAA

upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------gtaaggataaatctgaacttcttttctcctttatttgggagtt--ctatggcttttatagtgatactatattgtactg-tagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
                                           ||    |    |||||  | ||      | | ||   |  |   || | ||||   ||    |  |   || |  || ||||| |||||||| |||||||||||||| || |||||||||||| | |||||| |||| || |||   |||||||| ||||| || || ||| |||| || |
gtaagtcttttgttgtgatatttttttttgctcatcaggataatagtctttcccctgaatctgttactatatatgttccagcatctactcttgcttggctaacctttttcctttatggtgctagACAAAAGCAGGGCCAGTTTTGGTGGCTGTGAATCCTTTTAAGGAGGTTCCTTTATACGGAAATCGATACATTGAAGCATACAGGAAGAAATCAAATGAGA

upper sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------gtaaggataaatctgaacttcttttctcctttatttgggagttctatggctttt-------atagtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
              |  |   ||  | |||  ||| |        || |  |||  | ||   || |        || ||  |   || | |    | |||||| ||||||||| || ||| | || |||||||||||||||||||||||  | ||||||   ||     |  | || |||  ||| | |||    || |
tgtcttgttacattgcgatcctacttgtgactttcctcgtaatcgtagtgaggacatttaaaactctctctcagcatcgttgtggaatgtcgctacgcagACTAGAGCAGGTCCTGTCTTGATTGCAGTCAATCCTTTTAAGAAAGTTCCCATCTATGGTCCAGACAGTGTACAAGCTTATCAAAAGAGAACTCCAGAGA

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|29625634|gb|CB630645.1|CB630645
EST:     CATCCGTTCTGTACAATTTGCAGTACAGATACACTCAAGACTTGATATAT                         ACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCT
genomic: CATCCGTTCTGTACAATTTGCAGTACAGATACTCTCAAGACTTGATATATgtaaggataa ... tgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCT




















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: 72 (upstream exon), 69 (downstream exon)
Score: 31

AATTCTTGACGGGGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAGCCATCCGTTCTGTACAATTTGCAGTACAGATACTCTCAAGACTTGATATATgtaaggataa ... tgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcctttatttgggagttctatggcttttatagtgatactatattgtactgtagACTAAAGCAGGTCCAGTTTTGGTGGCGGTCAATCCTTTTAAGAAAGTTCCTCTATATGGTAATGAGTACATTGATGCATATAGAAATAAAACAAAGGATA
                                    atactatatt  TA-rich tract