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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTTTCTTCCCCAACAGTGGCATCCTCGCTGACCAAGGTGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaactaaaccacctctcctcgcattaattccattcggttgataagttcgtccagcaaatatttccttttctgattaagagctatatatatactcgtacgtcggccatatatacggggattccag

Basic information

species Zea mays
transcript GRMZM2G006578_T01
intron # 6
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|148961657|gb|EE012426.2|EE012426
EST:     TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAG                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
EST: gi|149032497|gb|EE154928.2|EE154928
EST:     TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAG                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
EST: gi|31355441|gb|CD439798.1|CD439798
EST:     TGTCGCCGGCAAAGGCGTCCCCATCCGTGGCATCGACGGCCTCAGCTCAG                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
EST: gi|148930796|gb|EC873148.2|EC873148
EST:     TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAG                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
EST: gi|148954298|gb|EC899706.2|EC899706
EST:     TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAG                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
EST: gi|149110645|gb|EE190527.2|EE190527
EST:     TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAG                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
EST: gi|76291953|gb|DV031521.1|DV031521
EST:     TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAG                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
EST: gi|67040862|gb|CO467117.1|CO467117
EST:     TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCTGCTCAC                         AGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC
genomic: TGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACC

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: 45 (upstream exon), 45 (downstream exon)
Score: 2

GGAGTTTTCTTCCCCAACAGTGGCATCCTCGCTGACCAAGGTGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACCGGCTGATGTACGAGCTTCGGGCGGCGCTGCAGCAGCACCTGCCGGAGGG


Block sizes: 42 (upstream exon), 39 (downstream exon)
Score: 8

GGAGTTTTCTTCCCCAACAGTGGCATCCTCGCTGACCAAGGTGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACCGGCTGATGTACGAGCTTCGGGCGGCGCTGCAGCAGCACCTGCCGGAGGG


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 24

GGAGTTTTCTTCCCCAACAGTGGCATCCTCGCTGACCAAGGTGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACCGGCTGATGTACGAGCTTCGGGCGGCGCTGCAGCAGCACCTGCCGGAGGG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 37

GGAGTTTTCTTCCCCAACAGTGGCATCCTCGCTGACCAAGGTGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaacta ... gggattccagAGGCGGCGATGTTCGACGTGGAGTACGGGCGGTGGCAGGAGGAGCACTACCGGCTGATGTACGAGCTTCGGGCGGCGCTGCAGCAGCACCTGCCGGAGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTTTTCTTCCCCAACAGTGGCATCCTCGCTGACCAAGGTGTCGCCGGCAAAGGCGTCCCCATCGGCGGCATCGACGGCCTCAGCTCAGgtacaaactaaaccacctctcctcgcattaattccattcggttgataagttcgtccagcaaatatttccttttctgattaagagctatatatatactcgtacgtcggccatatatacggggattccag

- - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA