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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCACCCCACTATTCCTTTCTGCTGAGCTCAGGAAATCCCCTCTGGTCTCCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccaccaccgaggcccctcttctccgcgtaccctgttgtagctgcctccctcgcgaggtccgcggtttcttttggccttttgctccgtttactag...

Basic information

species Zea mays
transcript GRMZM2G041881_T02
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|211164811|gb|FL068780.1|FL068780
EST:     CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGSGCCTGTTCAAG                         ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
genomic: CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
EST: gi|211164808|gb|FL068777.1|FL068777
EST:     CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGCTCAAG                         ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
genomic: CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
EST: gi|211164799|gb|FL068768.1|FL068768
EST:     -CCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAG                         ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
genomic: CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
EST: gi|211339244|gb|FL068784.1|FL068784
EST:     CCCCGT-CCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGCTCAAG                         ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
genomic: CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
EST: gi|14997050|gb|BI319140.1|BI319140
EST:     CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGCTCAAG                         ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
genomic: CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
EST: gi|211530342|gb|FL172605.1|FL172605
EST:     CCCCGTCCCCCATTCCACCCGCCGCCGNCGACGCGCCGCGCCTGCTCAAG                         ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
genomic: CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
EST: gi|76016587|gb|DT943757.1|DT943757
EST:     CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAG                         ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA
genomic: CCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 371

CCCCACCCCACTATTCCTTTCTGCTGAGCTCAGGAAATCCCCTCTGGTCTCCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 401

CCCCACCCCACTATTCCTTTCTGCTGAGCTCAGGAAATCCCCTCTGGTCTCCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 382

CCCCACCCCACTATTCCTTTCTGCTGAGCTCAGGAAATCCCCTCTGGTCTCCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 314

CCCCACCCCACTATTCCTTTCTGCTGAGCTCAGGAAATCCCCTCTGGTCTCCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccac ... cctcacgcagATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCACCCCACTATTCCTTTCTGCTGAGCTCAGGAAATCCCCTCTGGTCTCCCCGTCCCCCATTCCACCCGCCGCCGCCGACGCGCCGCGCCTGTTCAAGgtgagtccaccaccgaggcccctcttctccgcgtaccctgttgtagctgcctccctcgcgaggtccgcggtttcttttggccttttgctccgtttactag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctcgc