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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactttggcaagatggatacacatgtgtaggacaaaagctaacctatttctgatcaatttctttggtaaactatatcag

Basic information

species Oryza sativa
transcript LOC_Os07g12250.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12250.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA13G21520.1 (Glycine max), 5'ss of exon 2
GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtga------gtactttggcaagatggatacacatgtgtag--------gacaaaagctaacctatttc---tgatcaatttctttggtaaactatatcag------------------------------------------------------------
 || ||||||||||| |||||||| |||||||| ||||||||||| || ||||||||  | ||||  || || |||||||      ||   | |   || |        |||| | |        || |   | |   || |||    ||||  | |  | |  |||  |||    |                                                            
AACCGAGCTGTGCCGATTCAGCGGTGCCAAGATCTACCCAGGGAAAGGCATCAGATTTGTTCGTGGTGATTCTCAGgtgacaatatgtttctcgttgagttttgggttgatgtatcgtttcatttgaaactggatgttctgtttactatgatgcaatcatattataagttatgaggggttttgtttgttatttgttatgatactgatatgaggggttttgtttgttgaaacttacag

upper sequence: LOC_Os07g12250.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G07680.1 (Glycine max), 5'ss of exon 2
GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactttggcaagatggatacacatgtgtaggacaaaagctaacctatttctgatcaatttctttggtaaactatatcag-------------------------------------------------------------------------
 || || || ||||| |||||||| |||||||| ||||||||||| || ||||||||  | ||||  || || |||||||      |   | | |    |   |  | | ||   |    |    |  || ||||     | ||  ||  ||| |  ||                                                                          
AACCGAACTATGCCGATTCAGCGGTGCCAAGATCTACCCAGGGAAAGGCATCAGATTTGTTCGTGGTGATTCTCAGgtga----cataatatgtttctcattgaattttgggttgatgtattgtgttattttgatatggatgttctgtgtactttgacaaaatcatcatcaattttgatcgttttttactagttattatactgatataggggatttgtttgttgaatatacag
















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|88581534|gb|CI698528.1|CI698528
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88348866|gb|CI653910.1|CI653910
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|33670740|gb|CF298979.1|CF298979
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|24468910|gb|CA305859.1|CA305859
EST:     CCAAGATTTACCCTGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|109711943|gb|CI029113.1|CI029113
EST:     CAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88381633|gb|CI682300.1|CI682300
EST:     CAAGATTTACCCAGGGAAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CAAGATTTACCCAGGG-AAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|15853700|gb|BI806496.1|BI806496
EST:     GATTTACCCCAGGGAA-GGTATCAGATTCATCCG-GCAGACTCCCAG                         GTGTTCC-GTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: GATTTA-CCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88348364|gb|CI639023.1|CI639023
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88388417|gb|CI683189.1|CI683189
EST:     CAAGATTTACCCAGGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CAAGATTTACCCA-GGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88592045|gb|CI710122.1|CI710122
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88571275|gb|CI662648.1|CI662648
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|218483042|gb|FG956499.1|FG956499
EST:     CCAAGATTTACCCA-GGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|86898740|gb|CI296058.1|CI296058
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|3767629|gb|AU031656.1|AU031656
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|55441469|gb|CV734055.1|CV734055
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|55435894|gb|CV731084.1|CV731084
EST:     AGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: AGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88763039|gb|CI772595.1|CI772595
EST:     CCNAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|163927854|gb|EG713502.1|EG713502
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|112787065|gb|EE591987.1|EE591987
EST:     CCAAGATTTACCCTGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88290337|gb|CI665126.1|CI665126
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88739146|gb|CI762654.1|CI762654
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
EST: gi|88574546|gb|CI666315.1|CI666315
EST:     CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG                         GTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG
genomic: CCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTG

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: 75 (upstream exon), 74 (downstream exon)
Score: 58

GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAGgtgagtactt ... actatatcagGTGTTCCTGTTTTCAAACTCGAAGTGCAAGCGCTACTTCCACAACCGTCTGAAGCCAGCCAAGCTTACATGGACAGCCATGTACAGAAAGCAGCACAAGA




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