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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgctaccgaccggtggccgaccgtgtgttcttgtgtgtgcgctgggacggcggtgtacatgcgttgcaacagttgctgacgttgtgtcctggaatgtgatggtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCGATGAGCCCGGGGTGCACCGCGTGTGGCAGCCTAGCCGAGAGTCGCCGGG

Basic information

species Zea mays
transcript GRMZM2G069713_T02
intron # 2
splice site 3'
intron type U2

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|76012866|gb|DT940036.1|DT940036
EST:     CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCAC                         AGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTATACTGCCTCGCCG
genomic: CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
EST: gi|149087973|gb|EE287216.2|EE287216
EST:     CTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCAC                         AGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
genomic: CTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
EST: gi|78110759|gb|DV529157.1|DV529157
EST:     CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCAC                         AGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
genomic: CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
EST: gi|78087334|gb|DV515727.1|DV515727
EST:     CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCAC                         AGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
genomic: CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
EST: gi|74246502|gb|DT654416.1|DT654416
EST:     CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCAC                         AGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG
genomic: CGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCG

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: 29 (upstream exon), 49 (downstream exon)
Score: 14

GCCAACGTCGGCGACTCCCGGGCCGTGTTGGGCACCACGTCCGACGATGGCGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCGATGAGCCCGGGGTGCACCGCGTGTGGCAGCCTAGCCGAGAGTCGCCGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 26

GCCAACGTCGGCGACTCCCGGGCCGTGTTGGGCACCACGTCCGACGATGGCGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCGATGAGCCCGGGGTGCACCGCGTGTGGCAGCCTAGCCGAGAGTCGCCGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 33

GCCAACGTCGGCGACTCCCGGGCCGTGTTGGGCACCACGTCCGACGATGGCGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCGATGAGCCCGGGGTGCACCGCGTGTGGCAGCCTAGCCGAGAGTCGCCGGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 5

GCCAACGTCGGCGACTCCCGGGCCGTGTTGGGCACCACGTCCGACGATGGCGCCATTGCGGCTGTCCAGCTCACCGTCGACCTAAAGCCTAACCTGCCACgtaagtcgct ... gtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCGATGAGCCCGGGGTGCACCGCGTGTGGCAGCCTAGCCGAGAGTCGCCGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgcgttgcaacagttgctgacgttgtgtcctggaatgtgatggtgcatgcagAGGAGAAGGAGCGCATCCGGCGGTGCAATGGTCAAGTGTACTGCCTCGCCGATGAGCCCGGGGTGCACCGCGTGTGGCAGCCTAGCCGAGAGTCGCCGGG
                 tgctgac  putative branch site (score: 5)