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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccccttctttgcttccccaccgtcgttcgttcctcgcgttggatattccggaactgtagtcgtcggaaatgctaattcccgtcgtctccgtgcgggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGGTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG

Basic information

species Zea mays
transcript GRMZM2G327394_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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
















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|71766577|gb|DR964514.1|DR964514
EST:     GGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCC                         TACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGTCGCGCGG
genomic: GGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCCgtaagccccc ... gggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGG
EST: gi|211095159|gb|FL286932.1|FL286932
EST:     GGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCC                         TACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCTGCCGCGCGG
genomic: GGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCCgtaagccccc ... gggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

CGGCAACCCTGCTCCTCCGCCGGTGCCCTCCCGCACGATGAGCCGCAGCGGGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCCgtaagccccc ... gggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGGTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

CGGCAACCCTGCTCCTCCGCCGGTGCCCTCCCGCACGATGAGCCGCAGCGGGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCCgtaagccccc ... gggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGGTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

CGGCAACCCTGCTCCTCCGCCGGTGCCCTCCCGCACGATGAGCCGCAGCGGGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCCgtaagccccc ... gggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGGTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

CGGCAACCCTGCTCCTCCGCCGGTGCCCTCCCGCACGATGAGCCGCAGCGGGCCTCGCCGCGGCATCTTCGATGGCCTCCCCATCCCGGCCGACAAATCCgtaagccccc ... gggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGGTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggaactgtagtcgtcggaaatgctaattcccgtcgtctccgtgcgggggcgcagTACCTCAAGGAAAGCCTGTCGCGGATCGACGAGAGCTGGGCGGCCGCGCGGTTCGACTCGCTGCCGCACGTCGTGCACATCCTCACCTCCAAGGACCGCG
                     tgctaat  putative branch site (score: 84)
                        taatt  TA-rich tract