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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtcccctcctccctctcttgttatcctgtgcctctgggcggccggaggagcctgaattgttgtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGCTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG

Basic information

species Oryza sativa
transcript LOC_Os08g22864.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g22864.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G327394_T01 (Zea mays), 3'ss of exon 1
---------------------gtaagcgtcccctcctccctctcttgt-tatcctgtgcctctgggcggccggagg---agcctgaattgttgtcgt-------tgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGCTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG
                        | ||||      |||     |||  ||| | |   || | | || | | |     |       | ||   |||        |||||||||||||||| | || |||||||| |||||| | |||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||||
gtaagcccccttctttgcttccccaccgtcgttcgttcctcgcgttggatattccggaactgtagtcgtcggaaatgctaattcccgtcgtctccgtgcgggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGGTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG
















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|88327675|gb|CI657409.1|CI657409
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88444107|gb|CI594480.1|CI594480
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88719596|gb|CI743106.1|CI743106
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88365075|gb|CI616494.1|CI616494
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88727239|gb|CI750894.1|CI750894
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88431150|gb|CI574321.1|CI574321
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88306004|gb|CI635004.1|CI635004
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88391505|gb|CI598323.1|CI598323
EST:     GCGGCCGCCGCCGCGTCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|58669732|gb|CK058418.1|CK058418
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88358732|gb|CI649281.1|CI649281
EST:     GCGGCCGCCGCCGNATTTTCGACGGCCTCCCCAT-CCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC
EST: gi|88719158|gb|CI742668.1|CI742668
EST:     GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCC                         TACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGNGGCGCGC
genomic: GCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGC

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: 66 (upstream exon), 50 (downstream exon)
Score: 54

CCCCAACGGTTCCAGATCTCGCTTCGCCAGCGGCGCGATGAGCCGCACCGGCGGCCGCCGCCGCATCTTCGACGGCCTCCCCATCCCAGCCGACAAATCCgtaagcgtcc ... gtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGCTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttatcctgtgcctctgggcggccggaggagcctgaattgttgtcgttgcagTACCTCAAGGAAGGGCTCTCGCGGATTGACGAGGGGTGGGCGGCGGCGCGCTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG
                                      aattgtt  TA-rich tract