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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttcccttttctcggttcggtttggttggtgggggaagggggtaattctaattctgggcttgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC

Basic information

species Oryza sativa
transcript LOC_Os01g56890.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56890.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G132978_T01 (Zea mays), 3'ss of exon 1
--------gtgcgttcccttttctcggttcggttt-ggttgg--tgggggaagggggtaattctaattctgggct---tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC
           |    |||   | | | | | ||  ||||||  ||| ||    || |||||||     | || |   ||||| |||||||||| ||||||||||||||||| |||||||||||||  | | ||| || |||||||||||||||||||||||||| ||||| ||||| ||  ||||  
gtacgcatacacccctcctcccccctgcttgattgaggttgggttggtggggaaggctaattctggaggttggttggttgctccgcagCATCCGAATCCGATAGGGGAGGGGCTGGCCATGGAGGCGTTCGCGGAAGCCGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTCA

upper sequence: LOC_Os01g56890.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G127453_T02 (Zea mays), 3'ss of exon 1
----gtgcgttcccttttctcggttcggtttggttggtg--ggggaaggggg-taattctaattctgggct---tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC
    || ||  ||  |  | | | | | || || | |||  || || |  || |||||||     | || |   ||||| |||||||||||||||||| || |||||| |||| ||||||||  | | |||||| |||||||||||||||||||||||||| ||||| ||||| ||  ||||  
gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA
















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|88827005|gb|CI777570.1|CI777570
EST:     TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAG                         CATCCGGATCCGATAGGGG
genomic: TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGG
EST: gi|33799632|gb|CF325677.1|CF325677
EST:     TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAG                         CATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG
genomic: TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG
EST: gi|33797362|gb|CF324543.1|CF324543
EST:     GCCGTCATGAAG                         CATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG
genomic: GCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG

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), 60 (downstream exon)
Score: 50

CGGCGCCGCGGGGATCCGCCCCGTCCCGCGCATCCACCACGCCCCCGTCCTCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcggtttggttggtgggggaagggggtaattctaattctgggcttgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC
                              ttctaat  putative branch site (score: 50)
                                           cttgctct  putative PPT
                           taattctaatt  TA-rich tract