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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaagtaaccgaataaacatggttagtacttatttcctgttttcagacctgttgagcatgaactgatgcaaaccattttttttgtgtgtgccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG

Basic information

species Zea mays
transcript GRMZM2G039954_T04
intron # 1
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|211452545|gb|FK959195.1|FK959195
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211066312|gb|FK959235.1|FK959235
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211071802|gb|FK959273.1|FK959273
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|18181111|gb|BM382321.1|BM382321
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211066314|gb|FK959237.1|FK959237
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211302619|gb|FL366312.1|FL366312
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211454670|gb|FK959205.1|FK959205
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211071805|gb|FK959276.1|FK959276
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|161589394|gb|EY958626.1|EY958626
EST:     CGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCCTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: CGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211450408|gb|FK959184.1|FK959184
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211454673|gb|FK959208.1|FK959208
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGKCCGCTCCCGAGACTACTGCTGC                         TCCGATCCTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211074529|gb|FK959279.1|FK959279
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211456805|gb|FK959224.1|FK959224
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452548|gb|FK959198.1|FK959198
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|116824448|gb|EC868068.1|EC868068
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211454677|gb|FK959212.1|FK959212
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211069063|gb|FK959256.1|FK959256
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452546|gb|FK959196.1|FK959196
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211066317|gb|FK959240.1|FK959240
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211069066|gb|FK959259.1|FK959259
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211450407|gb|FK959183.1|FK959183
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211069060|gb|FK959253.1|FK959253
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211071803|gb|FK959274.1|FK959274
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452538|gb|FK959188.1|FK959188
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211069062|gb|FK959255.1|FK959255
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452540|gb|FK959190.1|FK959190
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452543|gb|FK959193.1|FK959193
EST:     GGCGCAT-CTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452544|gb|FK959194.1|FK959194
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452541|gb|FK959191.1|FK959191
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211452550|gb|FK959200.1|FK959200
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCCTGGAACATCCAGCAGAGGAACCAG--ATCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211066311|gb|FK959234.1|FK959234
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|116813303|gb|EC855734.1|EC855734
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGTGAACCAGACAGCGATCACGAGTTCA
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAG-GAACCAGACAGCGATCACGAGTTCA
EST: gi|211066318|gb|FK959241.1|FK959241
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGARGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211454668|gb|FK959203.1|FK959203
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211456803|gb|FK959222.1|FK959222
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
EST: gi|211074535|gb|FK959285.1|FK959285
EST:     GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGC                         TCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
genomic: GGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG

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), 17 (downstream exon)
Score: 7

GAGACGTCACGCCTGCGCGGCTGCGCCCACCATGGACGAGGAGGAGTTCCGGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 6

GAGACGTCACGCCTGCGCGGCTGCGCCCACCATGGACGAGGAGGAGTTCCGGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 11

GAGACGTCACGCCTGCGCGGCTGCGCCCACCATGGACGAGGAGGAGTTCCGGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG


Block sizes: 49 (upstream exon), 27 (downstream exon)
Score: 10

GAGACGTCACGCCTGCGCGGCTGCGCCCACCATGGACGAGGAGGAGTTCCGGCGCATGCTCGACCTCTTCCCGGTCGTCCGCTCCCGAGACTACTGCTGCgtaaacctcc ... ccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctgttgagcatgaactgatgcaaaccattttttttgtgtgtgccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG
               aactgat  putative branch site (score: 10)
                        aaaccatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaagtaaccgaataaacatggttagtacttatttcctgttttcagacctgttgagcatgaactgatgcaaaccattttttttgtgtgtgccaaatgtagTCCGATCTTGGAACATCCAGCAGAGGAACCAGACAGCGATCACGAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA