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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTCCAGATTCAGGAACTAGACTCCTCCGGTCCGGTCCTCCCCCTCCCGCCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtctgccccctcccctctttgggggggaaaaacttcccgccggcgctcggggtctggagcaccagttcttctaggatcgccgcgtggtttagg...

Basic information

species Zea mays
transcript GRMZM2G138907_T01
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|71318270|gb|DR795899.1|DR795899
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|148949983|gb|EC895503.2|EC895503
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|101386394|gb|EB815216.1|EB815216
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|211358765|gb|FL074500.1|FL074500
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|83279229|gb|DV943237.1|DV943237
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|148945328|gb|EC890545.2|EC890545
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|148931952|gb|EC875193.2|EC875193
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|211361417|gb|FL074505.1|FL074505
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCYATTCACTGCCAG                         AAT-GSGCTCAACAAGGAGTACACGTACGCGGA-STGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|211181476|gb|FL002110.1|FL002110
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|50337860|gb|CO532986.1|CO532986
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|76287580|gb|DV027148.1|DV027148
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|211181474|gb|FL002108.1|FL002108
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|211361419|gb|FL074507.1|FL074507
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|211181473|gb|FL002107.1|FL002107
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|76282746|gb|DV022314.1|DV022314
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|211361416|gb|FL074504.1|FL074504
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCYATTCACTGCCAG                         AAT-GSGCTCAACAAGGAGTACACGTACGCGGA-STGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|149071845|gb|EE160234.2|EE160234
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
EST: gi|78119627|gb|DV538011.1|DV538011
EST:     CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAG                         AATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA
genomic: CCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTA

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: 39 (upstream exon), 46 (downstream exon)
Score: 20

CTGTCCAGATTCAGGAACTAGACTCCTCCGGTCCGGTCCTCCCCCTCCCGCCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTACTGGCCGTTCGAGAAGCTGCGGGTCTCCATCACCGGGGCCGGCGGGTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

CTGTCCAGATTCAGGAACTAGACTCCTCCGGTCCGGTCCTCCCCCTCCCGCCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTACTGGCCGTTCGAGAAGCTGCGGGTCTCCATCACCGGGGCCGGCGGGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

CTGTCCAGATTCAGGAACTAGACTCCTCCGGTCCGGTCCTCCCCCTCCCGCCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTACTGGCCGTTCGAGAAGCTGCGGGTCTCCATCACCGGGGCCGGCGGGTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

CTGTCCAGATTCAGGAACTAGACTCCTCCGGTCCGGTCCTCCCCCTCCCGCCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtc ... gcgtgtgcagAATGGCGCTCAACAAGGAGTACACGTACGCGGAGCTGGAGAAGGAGCCGTACTGGCCGTTCGAGAAGCTGCGGGTCTCCATCACCGGGGCCGGCGGGTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTCCAGATTCAGGAACTAGACTCCTCCGGTCCGGTCCTCCCCCTCCCGCCCCGTCTCGCTCCAGCGGCTCCACGCCACCGTTTGCCATTCACTGCCAGgtatacagtctgccccctcccctctttgggggggaaaaacttcccgccggcgctcggggtctggagcaccagttcttctaggatcgccgcgtggtttagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccgcc