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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatgatgcccaccaccatcctctctctattcttttctttgcctccaccaattaattgtagcttaaaattttgacaagaaatcatgccatgtgtggtagttaaaattctgtggttacctttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g41460.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 3
gtatgtatgatgcccaccaccatcctctctctattcttttctttgcctccaccaattaattgtagcttaaaattttgacaagaaatcatgcca-tgtgtggtagttaaaattctgtggttacctttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
               ||  |         ||| | |||    |  | |  || |   || | ||||     |  | ||   | |||| |   | |||   |   | |    | |    || |  | |||| |   |   ||||| |||||||||||||||||||| ||| ||||||| |||||||||||| | ||||| ||||| |||||||||||||||||||| || |||||||| ||||||
-------------gtactgctccttatcttctttccttccaataacatttactaccaaaatatagc-----acgtggatccgcaatctttatactgtaccggcctcatctgtttaaaattgctctgttttgtgcctacattttttgtcaagCAAGTATGCCATCGCGACTTGAAGCTAGAGAACACCCTGTTGGACGGGAGCACCGCGCCTCGCCTCAAGATATGTGATTTTGGCTACTCAAAG

upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 3
gtatgtatgatgcccaccaccatcctctctctatt-cttttctttgcctccaccaattaattgtagcttaaaattttgacaagaaatcatgccatgtgtggtagttaaaattctgtggttacctttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
                         |   | ||||  |||||||||| ||||        ||    ||   ||| |  ||      ||  | |  || || |   ||||||             | ||||| |   |   | || |||||||||||||||||||||||| ||||||| |||||||||||| | ||||||||||| ||||||||| |||||||||| || || ||||| ||||||
------------------------gtacgtatattgtttttctttgcttccaatg-----ttactactgtcaatctgtactgc---tctggactggtctgtt---taaaatcgc-------ttctgtttttctgcctacctgttcgtcaagCAAGTATGCCATCGTGACTTGAAGCTAGAGAACACCCTGTTGGACGGCAGCACCGCGCCTCGCGTCAAGATATGTGATTTCGGCTACTCAAAG

upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081915_T02 (Zea mays), 3'ss of exon 3
gtatgtatgatgcccaccaccatcctctctctatt-cttttctttgcctccaccaattaattgtagcttaaaattttgacaagaaatcatgccatgtgtggtagttaaaattctgtggttacctttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
                         |   | ||||  |||||||||| ||||        ||    ||   ||| |  ||      ||  | |  || || |   ||||||             | ||||| |   |   | || |||||||||||||||||||||||| ||||||| |||||||||||| | ||||||||||| ||||||||| |||||||||| || || ||||| ||||  
------------------------gtacgtatattgtttttctttgcttccaatg-----ttactactgtcaatctgtactgc---tctggactggtctgtt---taaaatcgc-------ttctgtttttctgcctacctgTTCGTCAAGCAAGTATGCCATCGTGACTTGAAGCTAGAGAACACCCTGTTGGACGGCAGCACCGCGCCTCGCGTCAAGATATGTGATTTCGGCTACTCAA--

upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 4
gtatgtatg-atgcccaccaccatcctctctctattct----tttctttgc-ctccaccaattaattgtagcttaaaattttgacaagaaatcatgccatgtgtggtagtt---aaaattctgt--ggt-taccttttttttttt--ttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
|||  |    ||   | ||    | |||| || | |||    |   ||| | || |||  |    ||||||  || |       |||   || |      || |     ||   || ||| |||  | | || |  | || || |  | | | | ||    ||||||||||| ||||| ||| |||||||||| |||||  |||| || || ||| |||| |||||  | ||||||||||| ||||| || || |||
gtaattgaacattttcccctttctgctctgtccaatctaaattgagtttacactgcactgaaatgttgtagtatatatgacatgcaatgtattagtattagtattactcttttgaacattatgtctgatgtatcagtcttcttataatatgtctcttcacgaagCAAGTATGTCATCGGGACTTGAAGCTGGAAAACACTTTGCTGGATGGAAGCTCGGCACCTCGTTTAAAGATATGCGATTTTGGGTACTCCAAG

upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 4
gtatgtatgatgcccaccaccatcctctctctattcttttctttgcctccaccaattaattgtagcttaaaattttgacaaga--aatcatgccatgtgtggtagttaaaattctgtggttacctttttttttttttttttt-tttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
                                                                |   | || || | ||     | || |  |   |    ||| || |||    || | || |   | | | ||| | || |||  | ||||||||||||||||||||| ||||| ||||||||||  || | || || ||  | || |||||  | ||||| || || ||||| |||||||||
----------------------------------------------------------------gtacataagttcggcatctttagtctttactcttacaataggtataatgagttgctgacttgaatgtctatttatcttatttaataaagCAAGTATGCCATCGTGACTTGAAGTTGGAGAACACATTGTTGGATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGTATTCAAAG

upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 4
gtatgtatgatgcccaccaccatcctctctctattcttttctttgcctccaccaattaattgtagcttaaaattttgacaaga--aatcatgccatgtgtggtagttaaaattctgtggttacct---ttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
                                                                |   | || || | ||     | || |  | | |    ||| || |||    || | || |   | ||| | ||| | || |||  | ||||||||||||||||||||| ||||| ||||||||||  |||| || || ||  | || |||||  | ||||| || || ||||| ||||| |||
----------------------------------------------------------------gtacataagttcggcatctttagtctttacttttacaataggtataatgagttgctgacttcaatgtttctatttatcttatttaataaagCAAGTATGCCATCGTGACTTGAAGTTGGAGAACACATTGCTGGATGGTAGTCCAGCTCCTCGTTTGAAGATTTGTGATTTTGGGTATTCGAAG

upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ13672 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtatgatgcccaccaccatcctctctctattcttttctttgcctccaccaattaattgtagcttaaaattttgacaagaaatcatgccatgtgtggtagttaaaattctgtggtt---acctttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
                                                                                                ||   | ||  | |||| |  |    || ||| |  ||    | |    |  || || |||| ||||| || || || |||||||||||||| || |||||||||||| |||| || || ||||| || || ||||| ||||| ||||||
------------------------------------------------------------------------------------------------gtaacatttccacttcttttctccaaacttttctccttaacgtgtagcgtactctagGAAGTCTGCCACCGGGATCTAAAGCTGGAGAACACGCTACTCGACGGCAGCCCGGCTCCACGTCTCAAAATTTGTGACTTCGGCTACTCAAAG

upper sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ28967 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtatgatgcccaccaccatcctctctctattcttttctttgcctccaccaattaattgtagcttaaaattttgacaagaaatcatgccatgtgtggtagttaaaattctgtggtt---acctttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
                                                                                                ||   | ||  | |||| |  |    || | | |  ||    | |  | |  || || |||| ||||| || || || |||||||||||||| || |||||||||||| |||| || || ||||| || || ||||| ||||| ||||||
------------------------------------------------------------------------------------------------gtaacatttccacttctcttctccaaacttgtctccttaacgtgtagtgtactctagGAAGTCTGCCACCGGGATCTAAAGCTGGAGAACACGCTACTCGACGGCAGCCCGGCTCCACGTCTCAAAATTTGTGACTTCGGCTACTCAAAG

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|218478528|gb|FG963468.1|FG963468
EST:     GGTTCTTTTTCCAGCAACTGATTTCAGGAGTCAGCTATTGCCATTCCATG                         CAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGC
genomic: GGTTCTTTTTCCAGCAACTGATTTCAGGAGTCAGCTATTGCCATTCCATGgtatgtatga ... tttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGC




















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: 74 (upstream exon), 73 (downstream exon)
Score: 5

GCACGGTTCTTTTTCCAGCAACTGATTTCAGGAGTCAGCTATTGCCATTCCATGgtatgtatga ... tttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggtagttaaaattctgtggttacctttttttttttttttttttttggtcaagCAAGTATGCCATCGTGACCTGAAGCTGGAGAACACCCTGCTCGACGGCAGCACGGCGCCTCGCCTCAAGATATGCGACTTTGGCTATTCAAAG
              ttctgtggttaccttt  CT-rich tract
                   tggttacctttttttt  TA-rich tract