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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATCGGTCAGATGATGATTTTTCACGTTATTGCTTCTCATCCGCATATATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaataccatggcacatcaatcttccgctgaaattcactcttcagcgatcttatatgcttacctacttttaaatttaaatgttcttatatccgcag

Basic information

species Oryza sativa
transcript LOC_Os03g26080.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g26080.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G097987_T01 (Zea mays), 5'ss of exon 5
CTAATCGGTCAGATGATGATTTTTCACGTTATTGCTTCTCATCCGCATATATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaataccatggcacatcaatcttccgctgaaattcactcttcagcgatcttatatgcttacctacttttaaatttaaatgttcttatatccgcag
||||| |||||||||| ||||||||||| |||||||||||    ||||||||||| ||||||||||| ||||||||||||||| |||||||||| |||||| ||| |||     | ||  ||         ||||||| ||||   || ||||| ||||||||| ||| ||| |  ||    || ||            
CTAATAGGTCAGATGAAGATTTTTCACGGTATTGCTTCTCGATGGCATATATTGTGGCTCTACTGCATGACAGTCTTGGTGTATCACTGGATGATAAGAGgtaagcatattg-agtacgcca------tagtgaaatttactcccaagtgatctcatatgcttatctaatttaattttctcctgatcag----------

upper sequence: LOC_Os03g26080.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G056944_T01 (Zea mays), 5'ss of exon 5
CTAATCGGTCAGATGATGATTTTTCACGTTATTGCTTCTCATCCGCATATATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaataccatggcacatcaatcttccgctgaaattcactcttcagcgatcttatatgcttacctacttttaaatttaaatgttcttatatccgcag
||||| |||||||||| ||||||||||| |||||||||||    ||||| ||||| ||||||||||| ||||||||||||||||||||||||||||||||||||| |||     ||||  ||         ||||||| ||||   || |||||  |  ||| | ||| ||| |  ||    || ||            
CTAATAGGTCAGATGAGGATTTTTCACGGTATTGCTTCTCGATGGCATACATTGTGGCTCTACTGCATGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagcatatt-cagcacgcca------tagtgaaatttactcccaagtgatctagttcgctcatctaatttaattttctcctgatcag----------

upper sequence: LOC_Os03g26080.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA01G05750.1 (Glycine max), 5'ss of exon 7
CTAATCGGTCA-GATGATGATTTTTCACGTTATTGCTTCTCATCCGCATATATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaataccatggcacatcaatcttccgctgaaattcactcttcagcgatcttatatgcttacctacttttaa-atttaaatgttcttatatccgcag-------
 |   |  | | || || |||||    || ||||||||||| || ||||| ||||| ||||| || ||||||||||||||  |  |  |||||||  |||||      ||     ||   |   ||||     | | || | | |   | | | | |||   ||||   | || || |||||     | |  || | | |        
-TCTCCCATGATGAGGAAGATTTACTTCGGTATTGCTTCTCTTCAGCATACATTGTTGCTCTGCTTCACGACAGTCTTGGAATTGCTTTGGATGATGAGAGg------tattcctgcttgtttttcttttaaggtatttgaatatattgaggt-tgataacattacaggcattgaacatttaggccctttcgtacctgaaacaaacat

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|88958437|gb|CI095954.1|CI095954
EST:     TGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: TGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86828552|gb|CI278646.1|CI278646
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|87015611|gb|CI277569.1|CI277569
EST:     ATTGTAGCTATACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGACCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86500370|gb|CI143003.1|CI143003
EST:     TTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACCAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGG
genomic: TTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGA-CAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGG
EST: gi|87015604|gb|CI277562.1|CI277562
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCCTGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGG-CCCTGG
EST: gi|86505453|gb|CI148086.1|CI148086
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACCTCAAGTTGAATGGGCCCTGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACA-CTCAAGTTGAATGGGCCCTGG
EST: gi|86500357|gb|CI142990.1|CI142990
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|87015937|gb|CI279689.1|CI279689
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCCTGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGG-CCCTGG
EST: gi|88959341|gb|CI093036.1|CI093036
EST:     ATTGTAGCTTTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86501302|gb|CI143935.1|CI143935
EST:     TTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACCAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGG
genomic: TTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGA-CAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGG
EST: gi|86498791|gb|CI141424.1|CI141424
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|87021649|gb|CI276048.1|CI276048
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|88225174|gb|CI225090.1|CI225090
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|87026199|gb|CI278323.1|CI278323
EST:     ATTGTAGCTCTACTGCTCGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86499306|gb|CI141939.1|CI141939
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|88225813|gb|CI225729.1|CI225729
EST:     TTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: TTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86502869|gb|CI145502.1|CI145502
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|88959280|gb|CI092975.1|CI092975
EST:     TGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: TGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86501742|gb|CI144375.1|CI144375
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86498361|gb|CI140994.1|CI140994
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|89181030|gb|CI045113.1|CI045113
EST:     CGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: CGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86502691|gb|CI145324.1|CI145324
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86593841|gb|CI260070.1|CI260070
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|29685912|gb|CB682187.1|CB682187
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|88221597|gb|CI221553.1|CI221553
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86500132|gb|CI142765.1|CI142765
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|88225802|gb|CI225718.1|CI225718
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|86859213|gb|CI277100.1|CI277100
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
EST: gi|88222432|gb|CI222388.1|CI222388
EST:     ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAG                         GATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG
genomic: ATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGG

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: 60 (upstream exon), 59 (downstream exon)
Score: 13

CTAATCGGTCAGATGATGATTTTTCACGTTATTGCTTCTCATCCGCATATATTGTAGCTCTACTGCACGACAGTCTTGGTGTACCACTGGATGACAAGAGgcaagaatac ... atatccgcagGATTGAGTATTCAAATCAGGTTGGAGACACTCAAGTTGAATGGGCCCTGGGGGCTTTCATCTCAAACATAAAAGGCGTAATTGTAGAGCCATCAGCAACT




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