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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGCCGTCTGCGGCCCGCCCATCCGCAACCCATGGCTGTCGTCGAAGAAGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccctcctcgcgctcggccactactaccgcccctaccccactcgtggctggctggtgctcagtgaatcgggtgctggtggcttgctcatacgtt...

Basic information

species Zea mays
transcript GRMZM2G133624_T01
intron # 1
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|32797619|gb|CD949855.1|CD949855
EST:     GATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: GATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211436147|gb|FL367592.1|FL367592
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|76918516|gb|DV167329.1|DV167329
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|71765927|gb|DR963864.1|DR963864
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|71438300|gb|DR819350.1|DR819350
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211197900|gb|FL329055.1|FL329055
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGC
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGC
EST: gi|71435151|gb|DR816201.1|DR816201
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|32864226|gb|CF003908.1|CF003908
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211189090|gb|FL366153.1|FL366153
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211050008|gb|FL347973.1|FL347973
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCCTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211270715|gb|FL364943.1|FL364943
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|78089641|gb|DV518015.1|DV518015
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211133426|gb|FL346177.1|FL346177
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211218056|gb|FL310380.1|FL310380
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211320437|gb|FL345942.1|FL345942
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|71306393|gb|DR789338.1|DR789338
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211078378|gb|FL344979.1|FL344979
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|149015212|gb|EE044997.2|EE044997
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|71299221|gb|DR785609.1|DR785609
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|78108738|gb|DV527155.1|DV527155
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|149076434|gb|EE165057.2|EE165057
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211036126|gb|FL344517.1|FL344517
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211257634|gb|FL327800.1|FL327800
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211491420|gb|FL310086.1|FL310086
EST:     AGACGCTGCGGCG-YTNCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|76021436|gb|DT948606.1|DT948606
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211257312|gb|FL311217.1|FL311217
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211274567|gb|FL349919.1|FL349919
EST:     AGACGCTGCRGCGTCTGCAGATCCMGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|211465020|gb|FL331108.1|FL331108
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|71435313|gb|DR816363.1|DR816363
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|32798036|gb|CD950272.1|CD950272
EST:     GATCCTGCCGCCGCGTCCGATCCCGCNCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCT
genomic: GATCCCGCCGCCGCGTCCGATCCCGC-CGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCT
EST: gi|9794264|gb|BE552572.1|BE552572
EST:     GGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: GGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
EST: gi|71321226|gb|DR797322.1|DR797322
EST:     AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTG                         GCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG
genomic: AGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTG

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: 48 (upstream exon), 49 (downstream exon)
Score: 135

GCCGGCCGTCTGCGGCCCGCCCATCCGCAACCCATGGCTGTCGTCGAAGAAGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTGAACCTCCCCAGGATGGCAGCGCCCCACCCGTGGTTTCCTCTGACATGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

GCCGGCCGTCTGCGGCCCGCCCATCCGCAACCCATGGCTGTCGTCGAAGAAGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTGAACCTCCCCAGGATGGCAGCGCCCCACCCGTGGTTTCCTCTGACATGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

GCCGGCCGTCTGCGGCCCGCCCATCCGCAACCCATGGCTGTCGTCGAAGAAGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTGAACCTCCCCAGGATGGCAGCGCCCCACCCGTGGTTTCCTCTGACATGGA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 69

GCCGGCCGTCTGCGGCCCGCCCATCCGCAACCCATGGCTGTCGTCGAAGAAGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccc ... tgattctcagGCTCCAGCGAAAACGAGATCACAGTAGAAGAGGCTTCTTTCGTGCATTCTGAACCTCCCCAGGATGGCAGCGCCCCACCCGTGGTTTCCTCTGACATGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGCCGTCTGCGGCCCGCCCATCCGCAACCCATGGCTGTCGTCGAAGAAGACGCTGCGGCGTCTGCAGATCCCGCCGCCGCGTCCGATCCCGCCGCTGgtgagtaccctcctcgcgctcggccactactaccgcccctaccccactcgtggctggctggtgctcagtgaatcgggtgctggtggcttgctcatacgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgcccc