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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATACATGGCAAATAAGCTGATTTCCGGGACATGCCTTCAGCTTTTGCGACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcgttctcatcctcaacaatttctgtgggtaaatgagtttaagcaccatcatgtgatcgcttttccttaagagatttcatattgacttcttagtgctgattttgctgttttgtgcacttctgtttggctatggtaatttgcatttgcaactgttctcttgacataatgtccactggaaattcttttag

Basic information

species Oryza sativa
transcript LOC_Os07g36465.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g36465.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G163233_T01 (Zea mays), 5'ss of exon 6
ATCATACATGGCAAATAAGCTGATTTCCGGGACATGCCTTCAGCTTTTGCGACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcgttctcatcctcaacaatttctgtgggtaaatgagtttaagcaccatcatgtgatcgcttttccttaagagatttcatattgacttcttagtgctgattttgctgttttgtgcacttctgtttggctatggtaatttgcatttgcaactgttctcttgacataatgtccactggaaattcttttag
    |||||| ||| |||||| || ||||| || |||||||||||||| || || |||||||||||||| || ||||| |||| |||||| ||||| ||||| |||  | ||||||  || ||  |||| | ||||||||   | || |  |||||  | | |  || ||   ||   |  ||||| |||   || | | |                                                                                              
GCATTACATGTCAACTAAGCTTATCTCCGGAACGTGCCTTCAGCTTTTACGGCGATATGACCACAAACCGGAGAGCCAGCGAGCTCCTTTACTTGAGGAGgttagttgctttctcactctaaattatttatttgggtaaaaatgattgaagaccattgtatcactgccttctttttccatctttcagatttg-ttatgatt----------------------------------------------------------------------------------------------

upper sequence: LOC_Os07g36465.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G019999_T01 (Zea mays), 5'ss of exon 3
ATCATACATGGCAAATAAGCTGATTTCCGGGACATGCCTTCAGCTTTTGCGACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcgttctcatcctcaacaatttctgtgggtaaatgagtttaagcaccatcatgtgatcgcttttccttaagagatttcatattgacttcttagtgctgattttgctgttttgtgcacttctgtttggctatggtaatttgcatttgcaactgttctcttgacataatgtccactggaaattcttttag
    |||||| ||| |||||| || ||||| || |||||||||||||| || || |||||||||||||| || ||||| |||| |||||||||||| |||||||||  | |||||| ||  || | | | ||||||||||   | ||||  |||||    | |         ||||     ||   | |  |  | | ||   || |                                                                                        
GCATTACATGTCAACTAAGCTTATCTCCGGAACGTGCCTTCAGCTTTTACGGCGATATGACCACAAACCGGAGAGCCAGCGAGCTCCTTTGCTTGAGGAGgtgagttgctttctcaccc--aagattatttgtgggtaaaaatgattaactaccattgcatcactaa-----cttagtgccttctttttccatctttcagatttggt----------------------------------------------------------------------------------------
















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|2427819|gb|C72282.1|C72282
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTNC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
EST: gi|33663505|gb|CF294472.1|CF294472
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
EST: gi|88389201|gb|CI597999.1|CI597999
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
EST: gi|88449975|gb|CI572106.1|CI572106
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
EST: gi|88344988|gb|CI625834.1|CI625834
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
EST: gi|88417555|gb|CI581578.1|CI581578
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
EST: gi|58670310|gb|CK058996.1|CK058996
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
EST: gi|58659574|gb|CK048254.1|CK048254
EST:     GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGGGTGATGAG                         GATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC
genomic: GACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCC

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), 75 (downstream exon)
Score: 44

ATCATACATGGCAAATAAGCTGATTTCCGGGACATGCCTTCAGCTTTTGCGACGTTATGACCACAAACCAGAAAGCCAACGAGGTCCTTTGCTTGATGAGgtgagtgtcg ... attcttttagGATGGGCCATCCTATGTTCGAGTGTTCCTGAATATCTTGCGGAACATCTCCAAGGAAGATACTGTTGAATATGTGCTTGCCCTGATTGATGAGATGCTTG




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