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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtgctgccacaaccaaactatggttgagtgactgtactaaactagtaggctaacctagtacaatttcatctgacgcttgggttttgacaatgcagGAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCCATTGAGGG

Basic information

species Oryza sativa
transcript LOC_Os03g17120.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G044237_T01 (Zea mays), 3'ss of exon 5
----gtacagtgctgccacaaccaaactatggttgag-tgactgtactaaactagtaggctaac-ctagtacaatttcat-----------ctgacgcttgggttttgacaatgcagGAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCCATTGAGGG
    |||| |   ||  ||| ||||  ||||  || | |   |||   | | | ||  ||| |  ||| ||  || |  |           ||||      || |||| || || ||||||||||| |||||||||| | |||||||||||||||||||||||| ||  || ||||
gtaggtac-gcaatgatacagccaa--tatgactgggattcttgtttcacattggtctgctgatgctaatatgatatagtagagtgcctttctgatatacaggctttggcattgtagGAGGCACTTTTAAATTCACTACCTAGACTTGTGGGCTCACTGTCTTCTTCAGTTCAGGG
















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|88358225|gb|CI605150.1|CI605150
EST:     ATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAG                         GAGGGCANCTTGTAAATTCA
genomic: ATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAGgtacagtgct ... gacaatgcagGAGG-CA-CTTGTAAATTCA
EST: gi|29613226|gb|CB618239.1|CB618239
EST:     ATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAG                         GAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCC
genomic: ATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAGgtacagtgct ... gacaatgcagGAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCC
EST: gi|218494800|gb|FG943469.1|FG943469
EST:     ATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAG                         GAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCC
genomic: ATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAGgtacagtgct ... gacaatgcagGAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCC

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: 72 (upstream exon), 68 (downstream exon)
Score: 19

CTTCTTAATGTGAGCACAAATGACATACTGATCCAGTCCACTGGTGTTATTGGTCAGAGAATAAAGAAGgtacagtgct ... gacaatgcagGAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCCATTGAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagtaggctaacctagtacaatttcatctgacgcttgggttttgacaatgcagGAGGCACTTGTAAATTCACTTCATAGACTTGTGGGCTCACTGTCTTCATCCATTGAGGG
                  tacaattt  TA-rich tract