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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgcccagcttacctgctcttactatttcgttctcgcatctcactgaatctggaatctgttattttttacgtgtttattagctacttagcttcttt...

Basic information

species Oryza sativa
transcript LOC_Os01g14040.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14040.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G100260_T03 (Zea mays), 5'ss of exon 2
GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgcccagcttacctgctcttactatttcgttctcgcatctcactgaatctggaatctgttattttttacgt-gtttattagctacttagcttcttt---
|| ||||||||  | ||||| ||||| ||||| || |||||||| || ||||||||||||||||| ||||| ||| ||||||| |||||||||| |    |     | | | |  |  |  |  |  |  | |   | ||||  |    |  ||| ||    |    |   |||||  ||  ||| ||        
GTCGAGGGGCGAATAGTGTCTGCGATCGGCCCTGGACTCCTCGTTCTCGTCGGCGTCCACGAGGCGGACACGGACTCCGACGCCGACTACATgtataacactcttctcctttcattcgcc-tcccacttcctccagttactggttt---atactgctagccatcgtctcaattattgtctgtttacctatgactat

upper sequence: LOC_Os01g14040.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA15G08610.1 (Glycine max), 5'ss of exon 1
--------GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgcccagcttacctgctcttactatttcgttctcgcatctcactgaatctggaatctgttattttttacgtgtttattagctacttagcttcttt
        || || || ||  | || || | ||||||||||||||| |||||||| |||||  |||||||  ||||  ||||||||||||| || |||||||   |  ||| || |    | | |   | | |    ||  |  || |   |      |    |  | |||||| | | ||  ||               
CCGTCGAGGTCGAAGGCCGCATCGTCTCCGAGATTGGCCCCGGCCTTCTCGTCCTCGTCGGAATCCACGACTCCGATTCCGACGCCGACGCCGATTACATgt-catctccatctcattaccccctttcaatccaagttca-acttctcatcagtcattactcatcttattttacttttctaacag---------------
















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|88395326|gb|CI611243.1|CI611243
EST:     GTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT                         TTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
genomic: GTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgccc ... ccttacgcagTTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
EST: gi|88692898|gb|CI736473.1|CI736473
EST:     GTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT                         TTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
genomic: GTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgccc ... ccttacgcagTTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
EST: gi|86854057|gb|CI252048.1|CI252048
EST:     ACACCGACGCCGACGCTGACTACAT                         TTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
genomic: ACACCGACGCCGACGCTGACTACATgtgtgtgccc ... ccttacgcagTTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
EST: gi|58690528|gb|CK079215.1|CK079215
EST:     GTCCTTGTCGGCGTCCGCGAGGCCGACACCGACGCCGACGCTGACTACAT                         TTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
genomic: GTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgccc ... ccttacgcagTTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
EST: gi|88422041|gb|CI611661.1|CI611661
EST:     GTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACAT                         TTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA
genomic: GTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgccc ... ccttacgcagTTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAA

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: 62 (upstream exon), 63 (downstream exon)
Score: 11

GTGGAGGGGCGGGTGGTGTCGGCGATTGGCCCCGGCCTCCTCGTCCTTGTCGGCGTCCACGAGGCCGACACCGACGCCGACGCTGACTACATgtgtgtgccc ... ccttacgcagTTGTCGGAAGGTTCTGAACATGAGGCTATTTCCTAATGAGAAGACTGAAAAGGCATGGGATCAAAGT




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