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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtccaacgattcaacatatccttcacattttgcaattctagggattcttccatatctctgcgtgtttcaaaaataatgtactgagttctgaaataccttacccggaacttgcgccaatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAACAGATAAGGGAAAGGCTCGCCAAAGTGAGGTCATAAAAGAGTAATGATG

Basic information

species Oryza sativa
transcript LOC_Os03g01810.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G042552_T01 (Zea mays), 3'ss of exon 4
gtaatgtccaacgattcaacatatccttcacattttgcaattctagggattcttccatatctctgcgtgtttcaaaaataatgtactgagttctgaaataccttacccggaacttgcgccaatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAACAGATAAGGGAAAGGCTCGCCAAAGTGAGGTCATAAAAGAGTAATGATG---------
                           | | || ||      ||| | || ||||   || | |||  |||   |     || |  |||   |     |    |  |   |     |   | |||||||||||||||||| || || || || ||||||| |         ||||| || ||||||||||||||||| |||| |||||||||||| ||||    |||           
--------------------------gtaatatatta-gtccctatgtatccttctgcat-tgtgccggttcatatttagatttcttgaacacctctctgagcttgcactattggccattattgtgcagAGAACTGCTATAGCAGAGGCTGTTGATGACGGT---------GAGCTAGACCAGATAAGGGAAAGGCTTGCCAGAGTGAGGTCATAGAAGATAGCTGAACAAGGTCAGA
















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|88532874|gb|CI461321.1|CI461321
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|33666696|gb|CF297663.1|CF297663
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|88542242|gb|CI471559.1|CI471559
EST:     GATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|27547715|gb|CA767395.2|CA767395
EST:     GGAAGGAAAGGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGA-G-C----TTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|88544923|gb|CI472450.1|CI472450
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|218480097|gb|FG955250.1|FG955250
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGA-G-C----TTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|88554456|gb|CI484638.1|CI484638
EST:     TGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: TGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|86493096|gb|CI135729.1|CI135729
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|88979017|gb|CI025535.1|CI025535
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|55439582|gb|CV733101.1|CV733101
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|88548645|gb|CI476460.1|CI476460
EST:     GAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|112785790|gb|EE591423.1|EE591423
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGGAGCCGTCGATGACGATGACGACGACG
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACG
EST: gi|86542982|gb|CI183188.1|CI183188
EST:     GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
EST: gi|88536817|gb|CI464606.1|CI464606
EST:     GCAACCTTCAACAAGTGAACCTGCAGAG                         AGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA
genomic: GCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAA

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: 73 (upstream exon), 49 (downstream exon)
Score: 21

CCTCTCTGCAATTGCTGGGGAGACTGCCTCTGAGCTTCCAGACGCTGTCAGGAAGGAAAAGGAGAAGATGAAGCAACCTTCAACAAGTGAACCTGCAGAGgtaatgtcca ... caatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAACAGATAAGGGAAAGGCTCGCCAAAGTGAGGTCATAAAAGAGTAATGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaataatgtactgagttctgaaataccttacccggaacttgcgccaatgtgcagAGAACTGCTATTGCGGAAGCCGTCGATGACGATGACGATGACGAGCTTGAACAGATAAGGGAAAGGCTCGCCAAAGTGAGGTCATAAAAGAGTAATGATG
                         accttac  putative branch site (score: 21)
                   tgaaata  TA-rich tract