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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgaccgatccaatggatccaaggcgcgcgcgcgatttattcatccgttgattggttcgcctcctgaatgacccag

Basic information

species Zea mays
transcript GRMZM2G061950_T02
intron # 2
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|37379602|gb|CF626547.1|CF626547
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCCCGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCCGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|32799782|gb|CD952018.1|CD952018
EST:     GATCCGCGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACACTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|148959272|gb|EC905354.2|EC905354
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|14208237|gb|BG841915.1|BG841915
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGC-G
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|31557932|gb|CD527144.1|CD527144
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGATATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|28568972|gb|CB280847.1|CB280847
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|211291869|gb|FL363130.1|FL363130
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|32797007|gb|CD949243.1|CD949243
EST:     GATCCCCGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACACTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|37378094|gb|CF625705.1|CF625705
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCCGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|14244662|gb|BG842600.2|BG842600
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|149205514|gb|ES701110.1|ES701110
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|37374405|gb|CF623556.1|CF623556
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCCGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|149205542|gb|ES701138.1|ES701138
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|211440499|gb|FL341607.1|FL341607
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACACGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|32796790|gb|CD949026.1|CD949026
EST:     GATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACACTGGACCCCGCGGAGAGGGACGCGGTGCTG
genomic: GATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|37379833|gb|CF626682.1|CF626682
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCCGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|40334431|gb|CK368501.1|CK368501
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCCGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|37376042|gb|CF624517.1|CF624517
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGCTGGACCCCGCCGAGAGGGACGCGGTGCTG
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTG
EST: gi|40303683|gb|CK348070.1|CK348070
EST:     GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAG                         AGGGCGGTGATCCTGTGGACGC
genomic: GGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGC

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), 49 (downstream exon)
Score: 106

CAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTGGCGAACGAGGAGGCGAAGAAGAGCCACCCCGGCGGCCGCGCGCTGGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 434

CAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTGGCGAACGAGGAGGCGAAGAAGAGCCACCCCGGCGGCCGCGCGCTGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 316

CAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTGGCGAACGAGGAGGCGAAGAAGAGCCACCCCGGCGGCCGCGCGCTGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

CAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgacc ... aatgacccagAGGGCGGTGATCCTGTGGACGCTGGACCCCGCGGAGAGGGACGCGGTGCTGGCGAACGAGGAGGCGAAGAAGAGCCACCCCGGCGGCCGCGCGCTGGTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACGCCGCGCAGCGCCGCGCGATCCGCCGCGGCTACGCCGAGGCGTACGGGAAGGAGCTGCTCCGCGCTCTCGGCGACGAGATCCACGGCAAGTTCGAGgtaggtgaccgatccaatggatccaaggcgcgcgcgcgatttattcatccgttgattggttcgcctcctgaatgacccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC