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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataatgtgcatcctaaaattgaatgggaaacatattaactgaaactcccaaattaaattctatgaaaccataaattttttattattatttggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAACCTCTCGGCTGTGGTGACACTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 10
gataatgtgcatcctaaaattga--atg-ggaaacatattaactgaaactcccaaattaaattctatgaaaccataaattt--tttattat-tatttggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAACCTCTCGGCTGTGGTGACACTGGCAG
    || ||  |  ||||||  |  ||| ||  | |  |||| | |  ||   |  | ||||  |   |  |  |   |||  |||  | | ||||||   |  ||  || ||| |  || | ||||||||||||||| |||||||||||| |||||||| | || | |||||||||||||||
----at-tgatttataaaatccataatgtggtcatactttaagt-atgctttgatttgaaatgttggcatgcagtttttttaatttgctttgtatttgtactttagATTATAAAATCTGGTGTGAAGATTGGCTTGAAGCACTTCAAGCCTATAAAACCTTTGGGTTATGGTGACACTGGCAG
















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|29612810|gb|CB617823.1|CB617823
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|14571435|gb|BI118803.1|BI118803
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|29666947|gb|CB663222.1|CB663222
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|58587914|gb|CF986222.1|CF986222
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|29615865|gb|CB620877.1|CB620877
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|29686409|gb|CB682684.1|CB682684
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|29680789|gb|CB677064.1|CB677064
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|29613843|gb|CB618856.1|CB618856
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
EST: gi|29646469|gb|CB651476.1|CB651476
EST:     CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAG                         GCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA
genomic: CTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAA

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: 70 (upstream exon), 52 (downstream exon)
Score: 23

AGACCAGAGGATTTGTGGGCAATTCACTCAATGCGTGTTTCTCCAAAACCTCACAAACGGAATAACCCTTCTTGGATAGCTATAGAAAAGgtacgttaat ... tggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAACCTCTCGGCTGTGGTGACACTGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccaaattaaattctatgaaaccataaattttttattattatttggcatgcagGCTACAAATTTAGGGGAGAAGATTGGCTTGAAACACTTCAAGCCTGTAAAACCTCTCGGCTGTGGTGACACTGGCAG
     aaattaaattctatga  TA-rich tract