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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgacacagaacagtatagttgcttgcatcagatttgtactgctcagctaatggtaatgctatctttgtaatttgtatgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAACTTAGCAAAGAATTAAAGAAGACTGATGGAAGCAAAAAGTCAAGAATTTC

Basic information

species Zea mays
transcript GRMZM2G021270_T01
intron # 4
splice site 3'
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|28987485|gb|CB351658.1|CB351658
EST:     GGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAG                         TTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAAC
genomic: GGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAGgtatgtgaca ... atgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAAC
EST: gi|32937597|gb|CF042416.1|CF042416
EST:     GGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAG                         TTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAAC
genomic: GGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAGgtatgtgaca ... atgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAAC
EST: gi|33095886|gb|CF055880.1|CF055880
EST:     GGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAG                         TTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAAC
genomic: GGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAGgtatgtgaca ... atgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAAC

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: 47 (upstream exon), 47 (downstream exon)
Score: 446

GACAATCCGGCTTTTGATTCACAAACCAAGGAGACCTTGACCACTCGTCAGGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAGgtatgtgaca ... atgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAACTTAGCAAAGAATTAAAGAAGACTGATGGAAGCAAAAAGTCAAGAATTTC


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 33

GACAATCCGGCTTTTGATTCACAAACCAAGGAGACCTTGACCACTCGTCAGGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAGgtatgtgaca ... atgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAACTTAGCAAAGAATTAAAGAAGACTGATGGAAGCAAAAAGTCAAGAATTTC


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 76

GACAATCCGGCTTTTGATTCACAAACCAAGGAGACCTTGACCACTCGTCAGGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAGgtatgtgaca ... atgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAACTTAGCAAAGAATTAAAGAAGACTGATGGAAGCAAAAAGTCAAGAATTTC


Block sizes: 45 (upstream exon), 42 (downstream exon)
Score: 19

GACAATCCGGCTTTTGATTCACAAACCAAGGAGACCTTGACCACTCGTCAGGGAAGCTTTGGGTCAAAGTGTGAGCTTTCTAGTGATTTCCTCAAGAAAGgtatgtgaca ... atgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAACTTAGCAAAGAATTAAAGAAGACTGATGGAAGCAAAAAGTCAAGAATTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgtactgctcagctaatggtaatgctatctttgtaatttgtatgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAACTTAGCAAAGAATTAAAGAAGACTGATGGAAGCAAAAAGTCAAGAATTTC
              agctaat  putative branch site (score: 19)
                             tatctttgtaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgacacagaacagtatagttgcttgcatcagatttgtactgctcagctaatggtaatgctatctttgtaatttgtatgattgcagTTGAGAAATCTGGTGTAATTGAGAATGTCCTCTCTTGGGCTGATTTCAAACTTAGCAAAGAATTAAAGAAGACTGATGGAAGCAAAAAGTCAAGAATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA