Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagttttttttatcacatacctatagtttcacaagacaaccagccgcctaactccatgattctccttttatggctgacgctgaatatttgatgaatacgcag

Basic information

species Zea mays
transcript GRMZM2G115424_T03
intron # 4
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|60396717|gb|DN229583.1|DN229583
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|60400143|gb|DN232950.1|DN232950
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|93282514|gb|EB674778.1|EB674778
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|149088114|gb|EE177273.2|EE177273
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|211157431|gb|FL453590.1|FL453590
EST:     AGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AGAAAAAACTCCTAAAAGCAGCAACAAGACTAAC-AAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|7227633|gb|AW566274.1|AW566274
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|91869344|gb|EB400345.1|EB400345
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCANAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCC-AAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|76935015|gb|DV174136.1|DV174136
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCANAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|60342995|gb|DN209968.1|DN209968
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|87153397|gb|DY398186.1|DY398186
EST:     AAGAAAAAACTCNTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CTTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|37386070|gb|CF630209.1|CF630209
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|60343251|gb|DN210224.1|DN210224
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|18964582|gb|BM661089.1|BM661089
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|149088113|gb|EE287286.2|EE287286
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|4753351|gb|AI657256.1|AI657256
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCAC
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCAC
EST: gi|149013491|gb|EE042992.2|EE042992
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|29129876|gb|CB380580.1|CB380580
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|74232054|gb|DT639968.1|DT639968
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|74232055|gb|DT639969.1|DT639969
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGGAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|31354599|gb|CD438956.1|CD438956
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|21390188|gb|BQ528237.1|BQ528237
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|31406448|gb|CD485180.1|CD485180
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|17921531|gb|BM259182.1|BM259182
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|86466339|gb|DY232710.1|DY232710
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAGAG                         CCTTCACGCCAGGTAGAACCCATCTCCAGGGTCCCAAA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAA
EST: gi|17921939|gb|BM259590.1|BM259590
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|17921859|gb|BM259510.1|BM259510
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|22490368|gb|BU050291.1|BU050291
EST:     TAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCNCCTCCA
genomic: TAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|5108057|gb|AI739770.1|AI739770
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|60355339|gb|DN222312.1|DN222312
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|76935014|gb|DV174135.1|DV174135
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|22542674|gb|BU093112.1|BU093112
EST:     CTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: CTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|32857894|gb|CD997575.1|CD997575
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|149110861|gb|EE294360.2|EE294360
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAGAG                         CCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCATAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA
EST: gi|78544653|gb|DV622151.1|DV622151
EST:     AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAG                         CCTTCACGCCAGGTAGAACCCAACTCAAGGGTCCCAAAGATGCCACCTCCA
genomic: AAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCA

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: 33 (upstream exon), 49 (downstream exon)
Score: 203

TCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGGGGAGGAAGGTGAACCACAGGAAGACCATG


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 116

TCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGGGGAGGAAGGTGAACCACAGGAAGACCATG


Block sizes: 33 (upstream exon), 49 (downstream exon)
Score: 112

TCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGGGGAGGAAGGTGAACCACAGGAAGACCATG


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 57

TCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagtt ... gaatacgcagCCTTCACGCCAGGTAGAACCCAACTCCAGGGTCCCAAAGATGCCACCTCCAAAGGACGAGGAGAGTGAAGGGGAGGAAGGTGAACCACAGGAAGACCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGCAACAAGACTAACAAATCTGGCTCAAAGgtatatagttttttttatcacatacctatagtttcacaagacaaccagccgcctaactccatgattctccttttatggctgacgctgaatatttgatgaatacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA