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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGATCGTCGCCATCAGGAGGGCAGAGGGGAAGGAGGTGCGCGTCGCCAATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttgccagcattctactctgctttgcccctgttcctagattaatcctgctcagtttgagtggattttgttaattttttgctttttcgttcgttg...

Basic information

species Oryza sativa
transcript LOC_Os03g61710.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G458549_T01 (Zea mays), 5'ss of exon 2
CATGATCGTCGCCATCAGGAGGGCAGAGGGGAAGGAGGTGCGCGTCGCCAATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttgccagcattctactctgctttgcccctgttcctagattaatc-ctgctcagtttgag--tggattttgttaattttttgctttttcgt-tcgttg
|||||||||||||||| | |||||  | ||     ||||| | |||||||| |||||||||||||||||| |||| || ||||| |||||||| ||||||||      |||   |  || ||     | |       ||  ||      |  ||| || | | | |  |  |||| |    || ||||    ||| | ||    
CATGATCGTCGCCATCCGAAGGGCCAACGGCGCCCAGGTGAGGGTCGCCAACGTCGACGACAAGTACCCCCTCTGCGTTTACCCCGCCGACCCAGACAAGgtgctccctgct--ctatccacatccatctagatagattggtattgcggtttctgatccgatcggggcttcatttcggcggttatttggaggttcctatcac--

upper sequence: LOC_Os03g61710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G458549_T02 (Zea mays), 5'ss of exon 2
---------------------------------------------------------------CATGATCGTCGCCATCAGGAGGGCAGAGGGGAAGGAGGTGCGCGTCGCCAATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttgccagcattctactctgctttgcccctgttcctagattaatcctgctcagtttgagtggattttgttaattttttgctttttcgttcgttg
                                                               |||||||||||||||| | |||||  | ||     ||||| | |||||||| |||||||||||||||||| |||| || ||||| |||||||| ||||||||           ||   || ||||  |   |  |  |  ||||||  ||                                                  
TCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAACGGCGCCCAGgtgagggtcgccaacgtcgacgacaagtaccccctctgcgtttaccccgccgacccagacaaggt-----------gctccctgctcta-tccacatccat--ctagatagatt-------------------------------------------------
















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|29681135|gb|CB677410.1|CB677410
EST:     ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAG                         GAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
genomic: ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttg ... tttcatgcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
EST: gi|29681133|gb|CB677408.1|CB677408
EST:     ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAG                         GAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
genomic: ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttg ... tttcatgcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
EST: gi|58611982|gb|CK039694.1|CK039694
EST:     ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAG                         GAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
genomic: ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttg ... tttcatgcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
EST: gi|88452999|gb|CI574546.1|CI574546
EST:     ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAG                         GAAATTGACATAAAAAATCACAAATG
genomic: ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttg ... tttcatgcagGAAATTGACATAAAAAACCACAAATG
EST: gi|58695416|gb|CK084103.1|CK084103
EST:     ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAG                         GAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
genomic: ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttg ... tttcatgcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
EST: gi|40493179|gb|BX900637.1|BX900637
EST:     ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAG                         GGAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG
genomic: ATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttg ... tttcatgcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG

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: 73 (upstream exon), 47 (downstream exon)
Score: 23

CATGATCGTCGCCATCAGGAGGGCAGAGGGGAAGGAGGTGCGCGTCGCCAATGTCGACGACAAGTACCCCATCTGTGTCTACCCGGCCGACCCCGACAAGgttaattttg ... tttcatgcagGAAATTGACATAAAAAACCACAAATGGGGCCACTATTTCATGTGTGG




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