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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagttgaaagtttgtttacttggtgattgaatgcacaagtcactcgtatattcttgttagctatataatggccttgcaagtttatatatggcag...

Basic information

species Oryza sativa
transcript LOC_Os01g16970.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G052875_T02 (Zea mays), 5'ss of exon 10
GCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagtt-gaaagtttgtttacttggtgattgaatgcacaagtcactcgtatattcttgttagctatataatggccttgcaagtttatatatggcag--
|||||||||||||| ||||||||||| ||||| | ||||||||| || || |||||||||| |||||||| | |  | || ||||||||||| || |||||||||| | || |||| | |||| |||  ||| |||  |||   | | | |  |||| | |||||   | ||       | |  ||  || | | ||   |  
GCTTCTCGTGTTCGTAAGGAGTATGACGATGCCAACTCAAAGCTTTCAAAAATTCAGTCTAAGATATCCAATTTAGCTGAGAAGCTAAAACATGATTTTGgtaagttaatttgaaactctgttcactatgtggttggctgccataatgatttttatagt-ttgttgtttgtacttcacacct--aaagttgtttctgattgtc

upper sequence: LOC_Os01g16970.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AC213600.3_FGT002 (Zea mays), 5'ss of exon 10
GCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtc--agttgaaagtttgtttacttggtgattgaatgcacaagtcactcgtatattct-tgttagctatataatggccttgcaagtttatatatggcag
||||||| |||||| ||||||||||||||||| ||||||||||| || || |||||||||| |||||||| |||  | || ||||||||||| || ||||||||||   | |||||| | |||| |||   ||||||     | ||   | |   ||| | | |  |    |  | | |    ||   || |  || |     
GCTTCTCATGTTCGTAAGGAGTATGATGATGCTAGCTCAAAGCTTTCAAAAATTCAGTCTAAGATATCCAGTCTAGCTGAGAAGCTAAAACATGATTTTGgtaagtataatttgaaattctgttcactatttgattggtgctataatgaagtttcataatttgtactttaaacctgaagtttctgattgtctg-atgtaat--
















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|29627610|gb|CB632621.1|CB632621
EST:     TAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: TAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
EST: gi|29614303|gb|CB619316.1|CB619316
EST:     GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
EST: gi|29622278|gb|CB627289.1|CB627289
EST:     GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
EST: gi|29627609|gb|CB632620.1|CB632620
EST:     GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
EST: gi|88371457|gb|CI602635.1|CI602635
EST:     GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
EST: gi|29627670|gb|CB632681.1|CB632681
EST:     GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
EST: gi|58589761|gb|CF988069.1|CF988069
EST:     GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
EST: gi|29627671|gb|CB632682.1|CB632682
EST:     GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTG                         GTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG
genomic: GATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGG

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: 69 (upstream exon), 72 (downstream exon)
Score: 41

GCTTCTCGTGTTCGGAAGGAGTATGATGATGCAAGCTCAAAGCTGTCCAAGATTCAGTCTAGGATATCCACTCTGACAGATAAGCTAAAACACGACTTTGgtaagtcagt ... ttcttattagGTAAGGAGAAGGAGTTCTATTACTTTTATGATCAGTGCTTTGAGAGCAAGGAGGGCAA




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