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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGCTTGTGCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatacttgctgggcatatggtgcctatccatccctctgaattcactgcacctaacttcccggtaacctcatctgcttccag

Basic information

species Zea mays
transcript GRMZM2G457381_T01
intron # 21
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|211103913|gb|FL456517.1|FL456517
EST:     GCCTGCTGACTYTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGACGGCCCGCGCGGGA
genomic: GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA
EST: gi|211286063|gb|FL280411.1|FL280411
EST:     GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACC
genomic: GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACC
EST: gi|211407845|gb|FL027525.1|FL027525
EST:     GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGACGGCCCGCGCGGGA
genomic: GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA
EST: gi|166574141|gb|EG282803.1|EG282803
EST:     GCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGACGGCCCGCGCGGGA
genomic: GCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA
EST: gi|31363681|gb|CD448038.1|CD448038
EST:     GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGACGGCCCGCGCGGGA
genomic: GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA
EST: gi|31355268|gb|CD439625.1|CD439625
EST:     GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGACGGCCCGCGCGGGA
genomic: GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA
EST: gi|31406179|gb|CD484911.1|CD484911
EST:     GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA
genomic: GCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA
EST: gi|166550532|gb|EG200439.1|EG200439
EST:     CTGCAAAGCGACAAGAAGAAAG                         GAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGACGGCCCGCGCGGGA
genomic: CTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 242

ATGAGCTTGTGCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGAAGAAGGCGCCTGCTGCCAGGTCAAGAGCAACCGGGTCAGGTGGGAAGGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 59

ATGAGCTTGTGCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGAAGAAGGCGCCTGCTGCCAGGTCAAGAGCAACCGGGTCAGGTGGGAAGGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 61

ATGAGCTTGTGCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGAAGAAGGCGCCTGCTGCCAGGTCAAGAGCAACCGGGTCAGGTGGGAAGGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 108

ATGAGCTTGTGCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatac ... ctgcttccagGAATCCAAGTGCAGCTTGACCTGAAGAGCAATGGGGATGGCCCGCGCGGGAAGAAGGCGCCTGCTGCCAGGTCAAGAGCAACCGGGTCAGGTGGGAAGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGCTTGTGCCTGCTGACTCTACGCCGAAGCTGGACCTGCAAAGCGACAAGAAGAAAGgttcccatacttgctgggcatatggtgcctatccatccctctgaattcactgcacctaacttcccggtaacctcatctgcttccag

- - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA