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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGCATGAGGCGCCTCCTCGGCGGCTCCCTCGTCCTTTGTATCGCCGCGGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccggatctgtccacgcctgcactgctatctttcatcccatatttttctgttgtcttctgttgatgtggttcttgattcaacatttctcggggttgcag

Basic information

species Zea mays
transcript AC213600.3_FGT002
intron # 1
splice site 5'
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|15427042|gb|BI542864.1|BI542864
EST:     CTGGGCATACCCCCGCAAG                         ATTAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: CTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211470279|gb|FL336879.1|FL336879
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211091911|gb|FL362893.1|FL362893
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211133488|gb|FL236777.1|FL236777
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211391684|gb|FL461159.1|FL461159
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211531444|gb|FL327584.1|FL327584
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211389058|gb|FL461157.1|FL461157
EST:     GGTGGTGGAGTCCAAGCCGCCTCTGGACTCTCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|15499427|gb|BI595940.1|BI595940
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCCCCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211237696|gb|FL353195.1|FL353195
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211133487|gb|FL236776.1|FL236776
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
EST: gi|211262935|gb|FL345535.1|FL345535
EST:     GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAG                         ATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA
genomic: GGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCA

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: 46 (upstream exon), 48 (downstream exon)
Score: 134

GCAGGCATGAGGCGCCTCCTCGGCGGCTCCCTCGTCCTTTGTATCGCCGCGGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 109

GCAGGCATGAGGCGCCTCCTCGGCGGCTCCCTCGTCCTTTGTATCGCCGCGGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

GCAGGCATGAGGCGCCTCCTCGGCGGCTCCCTCGTCCTTTGTATCGCCGCGGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 157

GCAGGCATGAGGCGCCTCCTCGGCGGCTCCCTCGTCCTTTGTATCGCCGCGGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccgg ... ggggttgcagATGAGGCGTACTACATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGCATGAGGCGCCTCCTCGGCGGCTCCCTCGTCCTTTGTATCGCCGCGGTGGTGGAGTCCAAGCCGCCTCTCGACTCTCTGGGCATACCACCGCAAGgttcaaccggatctgtccacgcctgcactgctatctttcatcccatatttttctgttgtcttctgttgatgtggttcttgattcaacatttctcggggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG