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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatggacgcaacactctgttcaaacagacctgtgacttagtttgcaaaagaccgcattgaatatattattattctggaattgactcactagaggaaatttgattctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCCTCACTTGGGTGGAAGCGACGCCGATGATATATGAAGCGCAAGTCAACAA

Basic information

species Zea mays
transcript GRMZM5G856436_T02
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|211161884|gb|FL207305.1|FL207305
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAA
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAA
EST: gi|26558493|gb|CA830728.1|CA830728
EST:     GCACATGAGAAGAGCCAAAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|211161885|gb|FL207306.1|FL207306
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTT-ATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACA
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACA
EST: gi|22472703|gb|BU037183.1|BU037183
EST:     GCACATGAGAAGAGCCAAAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|211161891|gb|FL207312.1|FL207312
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|211161881|gb|FL207302.1|FL207302
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|16927653|gb|BM080722.1|BM080722
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|211458337|gb|FL363659.1|FL363659
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|14243210|gb|BG840951.2|BG840951
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|67017876|gb|CO446625.1|CO446625
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|113701952|gb|EE679456.1|EE679456
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTTCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|16917041|gb|BM073101.1|BM073101
EST:     GATCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|21389991|gb|BQ528040.1|BQ528040
EST:     GCACATGAGAAGAGCCAAAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|60341900|gb|DN208873.1|DN208873
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|31352331|gb|CD436688.1|CD436688
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTTTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|211161889|gb|FL207310.1|FL207310
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTAT-CTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGC-AATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|37376556|gb|CF624817.1|CF624817
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|31352347|gb|CD436704.1|CD436704
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|16925094|gb|BM078162.1|BM078162
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
EST: gi|31351127|gb|CD435484.1|CD435484
EST:     GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAG                         GTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC
genomic: GCTCATGAGAAGAGCCAGAGATACAAGGAAGGAAAGTTTATTCTGGAGAGgtgatggacg ... ttctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatatattattattctggaattgactcactagaggaaatttgattctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCCTCACTTGGGTGGAAGCGACGCCGATGATATATGAAGCGCAAGTCAACAA
     atattattattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatggacgcaacactctgttcaaacagacctgtgacttagtttgcaaaagaccgcattgaatatattattattctggaattgactcactagaggaaatttgattctaagcagGTACAAGGTGTCGGGCCCTGACGGAAGCCAATACTGGATTCCACAAGATCCTCACTTGGGTGGAAGCGACGCCGATGATATATGAAGCGCAAGTCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC