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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAACTGCTGAAGTATGATGTCTCACTGAAAAACAACGAGATGGCAATGAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttcatggtcatgagtatatgcaaagagacaatgctcataatagtttgctttgatatttgttgttcatgctaaggatgccacttactttatttg...

Basic information

species Zea mays
transcript GRMZM5G884316_T02
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|74232779|gb|DT640693.1|DT640693
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|148971069|gb|EE021910.2|EE021910
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|76021371|gb|DT948541.1|DT948541
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|78120001|gb|DV538385.1|DV538385
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|86471421|gb|DY237791.1|DY237791
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|71431443|gb|DR812493.1|DR812493
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|78105803|gb|DV524221.1|DV524221
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|89250255|gb|DY622041.1|DY622041
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGNNNNNNNAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|76918441|gb|DV167296.1|DV167296
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
EST: gi|88749926|gb|DY534067.1|DY534067
EST:     GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAG                         GTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT
genomic: GAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAAT

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: 43 (upstream exon), 43 (downstream exon)
Score: 34

GCTGAACTGCTGAAGTATGATGTCTCACTGAAAAACAACGAGATGGCAATGAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAATTCCAATGACATCAG


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 37

GCTGAACTGCTGAAGTATGATGTCTCACTGAAAAACAACGAGATGGCAATGAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAATTCCAATGACATCAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 38

GCTGAACTGCTGAAGTATGATGTCTCACTGAAAAACAACGAGATGGCAATGAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAATTCCAATGACATCAG


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 20

GCTGAACTGCTGAAGTATGATGTCTCACTGAAAAACAACGAGATGGCAATGAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttc ... gatgctacagGTCGCCCCACCAAGCTGCCATGATATTCCTCCACTTACCAGTGTTTCAAATTCCAATGACATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGAACTGCTGAAGTATGATGTCTCACTGAAAAACAACGAGATGGCAATGAGAAGTGTTCAGGAAGAGGGGTAATATTTACTCAGAGCAGCAAAGGAAGgtgctacttcatggtcatgagtatatgcaaagagacaatgctcataatagtttgctttgatatttgttgttcatgctaaggatgccacttactttatttg

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA