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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctgaattaacataaaccgccacttgaatctcctcttatgtacaatctctattctgtttctttcactgatagattgttgatcatgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAATAAAAAAAGATTCAAGTGTACTACCCCGTATTGGTGCACTTAGTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g25580.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 5
gtatgtctgaattaacataaaccgccacttgaatctcctcttatgtacaatctctattctgtttctttcactgatagattgttgatcatgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAATAAAAAAAGATTCAAGTGTACTACCCCGTATTGGTGCACTTAGTGAG
    || || |  |||||| ||  ||| |     ||  ||||||     ||   |  | || ||   |   |  | |  | ||  |  ||||| ||||| ||||||||||||||||||||| |||| |||||||||||| ||||||||||||| ||||||||||||||||| |||||||  ||||||||||||
----gtatgtac-aacatatacttccagtca---cttttcttata---gatacttgctttggtttcatattttttggcgtattacttgtgttgcagGGCATATGTGTTTTTCAGTTCTCCCGTACATAAAGAATTAGTTGCTCAAATAAAAAAGGATTCAAGTGTACTACCTCGTATTGCCGCACTTAGTGAG
















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|29689434|gb|CB685709.1|CB685709
EST:     ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAA                         GGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTACTTACTCAAAT
genomic: ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAAgtatgtctga ... catgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAAT
EST: gi|29634393|gb|CB639402.1|CB639402
EST:     ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAA                         GGCGTATGTGTTTTTCAGTTCTCCCATACAGAA
genomic: ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAAgtatgtctga ... catgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAA
EST: gi|33676893|gb|CF305132.1|CF305132
EST:     CCGTTATACAAGAA                         GGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAAT
genomic: CCGTTATACAAGAAgtatgtctga ... catgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAAT
EST: gi|58687532|gb|CK076219.1|CK076219
EST:     ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAA                         GGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAAT
genomic: ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAAgtatgtctga ... catgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAAT
EST: gi|117231551|gb|CT846912.1|CT846912
EST:     ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAA                         GGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAAT
genomic: ATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAAgtatgtctga ... catgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAAT

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: 56 (upstream exon), 69 (downstream exon)
Score: 28

CATTGGGATGTTCCTGAATGACATGTCCGGAAGAAATCCGTTATACAAGAAgtatgtctga ... catgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAATAAAAAAAGATTCAAGTGTACTACCCCGTATTGGTGCACTTAGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtacaatctctattctgtttctttcactgatagattgttgatcatgttgtagGGCGTATGTGTTTTTCAGTTCTCCCATACAGAAAGAATTAGTTACTCAAATAAAAAAAGATTCAAGTGTACTACCCCGTATTGGTGCACTTAGTGAG
                    tttcttt  TA-rich tract