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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataattcttcttgttcttgttcttcatcttgttcgttttgctcggcggcttctcgcctgacgcgaggggtggtggtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os07g38530.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g38530.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G089159_T01 (Zea mays), 5'ss of exon 2
TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagat--aattcttcttgttcttgttcttcatcttgttcgttttgctcggcggcttctcgcctgacgcgaggggtg-----gtggtgtgcag
| || |||||||||||||||||||||||||||||  |||||||||      ||  |    |     || | |  | |   | ||||| | |  ||     |||||  ||||| | |     | ||  |||||
TTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGTgtaagatccggcgctgttctcgccaaagctgcgtgctttcaatcttgcttgcccactgagtccctgatccgaggtgcgtgtgcggggactgcag

upper sequence: LOC_Os07g38530.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G034779_T01 (Zea mays), 5'ss of exon 2
TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagata----attcttcttgttcttgtt-cttcatcttgttcgttttgctcggcggcttct-cgcctgacgcgaggggtg-----gtggtgtgcag
| || |||||||||||||||||||||||||||||  |||||||||       | |||| |     | | | |  | |  ||  | ||||    ||  ||     |||||  ||||| | |     | ||  |||||
TTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGTgtaagatccggcgctgttctcgccaaagctgcgtgctttcatttctcttgccgtccgagttgagtccctgatccgaggtgcgtgtgcggggactgcag
















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|58652513|gb|CK041193.1|CK041193
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGGTGCCAGGGGATGGAGGTGGCGTGGAACCAGG
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGA-GTACCAGGGGATGGAGGTGGCGTGGAACCAGG
EST: gi|88394443|gb|CI605784.1|CI605784
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
EST: gi|58658300|gb|CK046980.1|CK046980
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
EST: gi|29629432|gb|CB634441.1|CB634441
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
EST: gi|29622036|gb|CB627047.1|CB627047
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
EST: gi|88583784|gb|CI701291.1|CI701291
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
EST: gi|29629006|gb|CB634017.1|CB634017
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
EST: gi|88423128|gb|CI613429.1|CI613429
EST:     TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT                         GTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT
genomic: TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGT

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: 38 (upstream exon), 60 (downstream exon)
Score: 9

TACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGTgtaagataat ... tggtgtgcagGTACAGGGCGTTCGACGAGTACCAGGGGATGGAGGTGGCGTGGAACCAGGTGAAGCTGCACGACTTCCTGCAGAGCCCAGAGGACCTGGAGCGGCTCTAC




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