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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGTCATGGAAGAAATGAATGTTAAGACTGTCACTCCATGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAGgtatgtgtacctaatagcgtgagaaactttgcatttttttttatctactgctcagcacttgtgttattttcttag

Basic information

species Oryza sativa
transcript LOC_Os06g43760.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43760.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G348666_T02 (Zea mays), 5'ss of exon 18
TATGTCATGGAAGAAATGAATGTTAAGACTGTCACTCCATGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAGgtatgtgtacctaatagcgtgaga-aactttgcatttttttttatctactgctcagcacttgtgttattttcttag-------------------------
||||||||||| ||||| |||||||||| |||||||||||||||||| ||| || ||||||||||||| || || || || ||||| |||||||  ||  |  | | | |    |  |          |||   | | |  | |    |||| |||  | | | |                         
TATGTCATGGAGGAAATCAATGTTAAGAATGTCACTCCATGTAATGACCCCTTGATGTATGCTTCTCTGCGAGCCGAGCCTAATTTCAGgtatgattaagtgtttgagagccttaggtcaaggcaggatttgggccagtagttaatg-ttgttttaggtgcgtgggcaggccctactcagtatctctctt

upper sequence: LOC_Os06g43760.1 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G158627_T03 (Zea mays), 5'ss of exon 6
TATGTCATGGAAGAAATGAATGTTAAGACTGTCACTCCATGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAGgtatgtgtacctaatagcgtgagaaactttgcatttttttttatctactgctcagcacttgtgttattttcttag
||||||||||| ||||| ||||||||||||||||||||||| ||||| ||| || ||||||||||||| || || ||||| ||||| |||||||  ||  | |  ||   | | |||   ||||    |  | | ||||||||   |||||| ||||| |||||
TATGTCATGGAGGAAATCAATGTTAAGACTGTCACTCCATGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattagttcaatgcac-aaatactgcacatt----tgcacccactgctcaatgcttgtggtattt-cttag
















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|38476922|gb|CF961055.1|CF961055
EST:     TGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAG                         TGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGT
genomic: TGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAGgtatgtgtac ... attttcttagTGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGT
EST: gi|58672697|gb|CK061383.1|CK061383
EST:     TGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAG                         TGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGT
genomic: TGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAGgtatgtgtac ... attttcttagTGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGT
EST: gi|33690900|gb|CF319139.1|CF319139
EST:     TGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAG                         TGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGT
genomic: TGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAGgtatgtgtac ... attttcttagTGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGT

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: 75 (upstream exon), 70 (downstream exon)
Score: 58

TATGTCATGGAAGAAATGAATGTTAAGACTGTCACTCCATGTAATGATCCCATGTTGTATGCTTCTCTCCGGGCAGAACCCAATTTTAGgtatgtgtac ... attttcttagTGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGTGAAGAAAATGACACAGGAACAGATCTTAGCCTTTGAACAAAGTGGAGAA




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