Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatgattacctaacctatcgaccaaaatagatgttagctcctcaaacaagtttgttccttgttttctgttatcttccagatcttttccttttttt...

Basic information

species Zea mays
transcript GRMZM2G037743_T02
intron # 2
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|4834957|gb|AI670183.1|AI670183
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|60399258|gb|DN232072.1|DN232072
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|71307535|gb|DR789986.1|DR789986
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211032355|gb|FL404689.1|FL404689
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211034438|gb|FL381557.1|FL381557
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|60339444|gb|DN206417.1|DN206417
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|78026862|gb|DV495249.1|DV495249
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211277143|gb|FL403154.1|FL403154
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211401579|gb|FL440168.1|FL440168
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211264292|gb|FL408789.1|FL408789
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|50330964|gb|CO526090.1|CO526090
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211463969|gb|FL402454.1|FL402454
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTTGTCGTT
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTT-GTCGTT
EST: gi|211363155|gb|FL382231.1|FL382231
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATN                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211518774|gb|FL409538.1|FL409538
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211334965|gb|FL423295.1|FL423295
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|60344084|gb|DN211057.1|DN211057
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211207325|gb|FL408317.1|FL408317
EST:     ATCATCCTCGTGCAGAAGAWAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211374539|gb|FL412450.1|FL412450
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTTAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211063342|gb|FL405199.1|FL405199
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211332698|gb|FL418372.1|FL418372
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|211288084|gb|FL387842.1|FL387842
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
EST: gi|60357036|gb|DN224009.1|DN224009
EST:     ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATG                         GTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA
genomic: ATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACA

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: 46 (upstream exon), 44 (downstream exon)
Score: 119

ATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACAAATGGCGATTGGGAGGATTTCTCATACCACAAGTGTCTCCGGGCATACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

ATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACAAATGGCGATTGGGAGGATTTCTCATACCACAAGTGTCTCCGGGCATACC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 94

ATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACAAATGGCGATTGGGAGGATTTCTCATACCACAAGTGTCTCCGGGCATACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

ATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatga ... ttttgaaaagGTTGACAGGCACCCTGAGTTCAAGTCAAGATGTCTCTTTGTCGTTAGAACAAATGGCGATTGGGAGGATTTCTCATACCACAAGTGTCTCCGGGCATACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTTAAGCCCAGATGATGAAAAGGTTGTAAGAGAAAAGCTTCTTTCTCATCATCCTCGTGCAGAAGAAAAGATTGGTTGTGGGCTTGATGGTATAATGgtgagcatgattacctaacctatcgaccaaaatagatgttagctcctcaaacaagtttgttccttgttttctgttatcttccagatcttttccttttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacaag