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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaacaccactcacctttgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcag

Basic information

species Oryza sativa
transcript LOC_Os03g01850.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 7
GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaacaccactcacctt-tgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcag
|  || |||||  | ||||| | ||||||||||||||| |||||||||||||||||||||| ||      || |||  || ||||        | | ||| | ||| |    | || |  | || ||| |  | | ||  ||  ||| |||
GACCTGGCAACAGTAGTCCCAAATCTTGACCCTGCTGGGTTGGACCTTCTCTCTgtaagtcaaatggatttctcctgatgatcatggctgctgcttcatacatccctc----acagtattgaat-tcacc--tatttctgtttgctgacag

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 8
GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaacaccactcacctt-tgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcag
|  || ||||| || ||||| | ||| || |||||||| |||||||||||||||||||||| ||      ||   |  || |||| | |    ||| |||||   || |     |    | |    || |  ||| ||  |   ||| |||
GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaatggatttctgttgatgatcatgaccgctgcatcatatatatcctctctgtattgaatt----cacc--tgtttccgtctgctgacag
















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|33803869|gb|CF327809.1|CF327809
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88268788|gb|CI378723.1|CI378723
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|3766971|gb|AU031081.1|AU031081
EST:     TTGCAANTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|29662032|gb|CB658307.1|CB658307
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88446676|gb|CI526509.1|CI526509
EST:     GTCCCTACTCTTGACCCTGCTGG-TTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGGTAGACAGGCTCTT
genomic: GTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88559037|gb|CI489575.1|CI489575
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGNTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88253212|gb|CI351838.1|CI351838
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAAACAAAAAGGATCACAGCTAGACAGGCTC
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAA-CAAAA-GGATCACAGCTAGACAGGCTC
EST: gi|88978284|gb|CI384727.1|CI384727
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|86885548|gb|CI318699.1|CI318699
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCCGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|89196147|gb|CI397149.1|CI397149
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88437700|gb|CI531259.1|CI531259
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAAT-GCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCT
EST: gi|88488941|gb|CI426212.1|CI426212
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88509819|gb|CI437325.1|CI437325
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCANACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88437696|gb|CI531255.1|CI531255
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|38482398|gb|CF966438.1|CF966438
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|66915263|gb|CX102111.1|CX102111
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
EST: gi|88522726|gb|CI450366.1|CI450366
EST:     TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCT                         AAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT
genomic: TTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTT

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: 51 (upstream exon), 67 (downstream exon)
Score: 28

GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTCTCTgtaagtcgaa ... tcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAGTACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG




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