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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccacacactatcttatcccccatcttcctgcgcgcgacccataaccaatcccaagtagacgctgcgcattgtgtcagcctgccatggcttgacattgatagcgtcgtcttctgatgttcgtcag

Basic information

species Zea mays
transcript GRMZM2G047143_T02
intron # 3
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|31406271|gb|CD485003.1|CD485003
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|76019513|gb|DT946683.1|DT946683
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|34391357|gb|CF384585.1|CF384585
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|101396573|gb|EB820212.1|EB820212
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|87155980|gb|DY400769.1|DY400769
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|31441067|gb|CD510498.1|CD510498
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|101396571|gb|EB820211.1|EB820211
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|211437588|gb|FL436643.1|FL436643
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|148946894|gb|EC892174.2|EC892174
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|78078551|gb|DV506963.1|DV506963
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|5713718|gb|AI943710.1|AI943710
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|60349178|gb|DN216151.1|DN216151
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|94475186|gb|EB704144.1|EB704144
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|78023687|gb|DV492074.1|DV492074
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|12969132|gb|BG266077.1|BG266077
EST:     CGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: CGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|4966592|gb|AI691448.1|AI691448
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT
EST: gi|32912163|gb|CF016975.1|CF016975
EST:     GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGG                         GGCCATCAAGGAGAAGAGCGATAAGGAGATCATGAGGGAGATCCAGGCCAT
genomic: GAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCAT

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), 47 (downstream exon)
Score: 195

TGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 20

TGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 21

TGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 18

TGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccaca ... tgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGACGCCGAGGTCGTCGAGAAGGGgtgcgccacacactatcttatcccccatcttcctgcgcgcgacccataaccaatcccaagtagacgctgcgcattgtgtcagcctgccatggcttgacattgatagcgtcgtcttctgatgttcgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA