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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggacgtccctcttccttcctcacatccttctctatccgcaccctcttcgccttaaatcttatcttctcttctttggtttggaagcttctctcttttggccttaaccttagtacggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGGTGATCCACATCCGGAACGTCGGGCACGAAATCGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os05g36120.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G052926_T02 (Zea mays), 3'ss of exon 1
gtacggacgtccctcttccttcctcacatccttctctatccg--caccctcttcgccttaaatcttatcttctcttctttggtttggaagcttctctcttttggccttaaccttagtacggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGGTGATCCACATCCGGAACGTCGGGCACGAAATCGCTGAG
                       | |  |   |  | |   |         || ||  || ||||  |||||||  | ||   | |  || ||| |      | ||     ||| ||    ||     || | |||||| |   ||||||      ||||||| | |||||||| ||||| ||||||||||| |||||||||||||| || || |||
----------------------gtaatgtttgttgccagaagattggagctttggctgtagatctc-tcttctccccgtttcctcgatagtttcgcgacc--gaccaatttcttggtgatttttggctgttg-cctgtgttacagTGCGG------GAGGATGTCAGAGCCGTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG

upper sequence: LOC_Os05g36120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G070113_T01 (Zea mays), 3'ss of exon 1
gtacggacgtccctcttccttcc-tcacatccttctctatccgcaccctcttcgccttaaatcttatcttctcttctttggtttggaagcttctctcttttggccttaaccttagtacggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGGTGATCCACATCCGGAACGTCGGGCACGAAATCGCTGAG
      ||||  ||   ||     | | | | ||  || |  |  | |||||| ||            ||  ||   |||||| || | ||||   | |  | ||   |  || ||   ||  |  ||  |  |||   |||| | | ||||||| |||||| ||||||| || ||||| ||||||||||| |||||||||||||| || || |||
---gtaacgtttcttgcccggagattagagctttggctcta-gatctctcttctccccg---------tttcctcgattggttcgggaccttc---catacgacc---aatttcgtggtgtatattggctg--ctgcc-tgtgttacagTGCGGG-AGGATGTCGGAGCCTTCCAAGGTAATCCACATCCGCAACGTCGGGCACGAGATTGCCGAG
















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|88730256|gb|CI753870.1|CI753870
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
EST: gi|88422008|gb|CI611628.1|CI611628
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
EST: gi|88404556|gb|CI580992.1|CI580992
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
EST: gi|58676544|gb|CK065231.1|CK065231
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGTGCGGGGAGGATGGCGGAGCCGTC
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGT-G-GT-GT--GGTGCGGTGCGGGGAGGATGGCGGAGCCGTC
EST: gi|88358652|gb|CI617950.1|CI617950
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
EST: gi|88404569|gb|CI581005.1|CI581005
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGGCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
EST: gi|218493188|gb|FG964288.1|FG964288
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCC-----G------                         GTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
EST: gi|58602965|gb|CK013493.1|CK013493
EST:     GGCGGTGCCGGTGCCGGCGT-CTGCTGCTTCCGCCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGTGCGGGGAGGATGGCGGAGCCGTC
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGT-G-GT-GT--GGTGCGGTGCGGGGAGGATGGCGGAGCCGTC
EST: gi|88721255|gb|CI744554.1|CI744554
EST:     GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCC                         GTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG
genomic: GGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGG

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: 72 (upstream exon), 73 (downstream exon)
Score: 25

TTCACCCGCCGCCTCCGCGCCGATCTCATCTCCATCCCCCCGCGAGCAGCGGCGGTGCCGGTGCCGGCGTCCTGCTGCTTCCGCCGCCGGTGAGCACCCCgtacggacgt ... cggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGGTGATCCACATCCGGAACGTCGGGCACGAAATCGCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttggtttggaagcttctctcttttggccttaaccttagtacggttaacagGTAGACCTGTGGTGTGGTGCGGTGCGGGGAGGATGGCGGAGCCGTCTAAGGTGATCCACATCCGGAACGTCGGGCACGAAATCGCTGAG
                               ccttaac  putative branch site (score: 25)