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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgtagtgattagttgctgaaaaaatgtaatatgccctgttgaagataaatatgaccaatacttttgtgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCAACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG

Basic information

species Zea mays
transcript GRMZM2G553379_T04
intron # 3
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|71316728|gb|DR795038.1|DR795038
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|18659149|gb|BM500180.1|BM500180
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTTCAGC
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTT-CAGC
EST: gi|76913834|gb|DV165273.1|DV165273
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|74232113|gb|DT640027.1|DT640027
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGATTCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|50323594|gb|CO518720.1|CO518720
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|76011626|gb|DT938796.1|DT938796
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAA-TGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|76292653|gb|DV032221.1|DV032221
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|91868416|gb|EB400027.1|EB400027
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|26559940|gb|CA832175.1|CA832175
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGNGGAGAGGATCTTNGAAACGTTNGAATCTCAAAGAGCTTCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATG-GGAGAGGATCTT-GAAACGTT-GAATCTCAAAGAGCTTCA
EST: gi|67016868|gb|CO445617.1|CO445617
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|148980413|gb|EE027124.2|EE027124
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|87157251|gb|DY402040.1|DY402040
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGA-TCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|76909290|gb|DV163312.1|DV163312
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|71306906|gb|DR789609.1|DR789609
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCT
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCT
EST: gi|78082314|gb|DV510726.1|DV510726
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|76020109|gb|DT947279.1|DT947279
EST:     GAGTATAGAACACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCCAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCT
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCT
EST: gi|71325989|gb|DR799677.1|DR799677
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|149001052|gb|EE038303.2|EE038303
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|76932876|gb|DV173214.1|DV173214
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTG
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTG
EST: gi|149079785|gb|EE168784.2|EE168784
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|50325812|gb|CO520938.1|CO520938
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTC
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTC
EST: gi|149083438|gb|EE172758.2|EE172758
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|74242354|gb|DT650268.1|DT650268
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|50325934|gb|CO521060.1|CO521060
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|71425445|gb|DR806675.1|DR806675
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|78088356|gb|DV516749.1|DV516749
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|76011625|gb|DT938795.1|DT938795
EST:     AATAC-AAAATGTCAAAA                         GCACCTCATGGGAGAGGATC-TGNAAACG-TGAAATCTCAAAGAGCTTCAG
genomic: AATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTG-AAACGTTG-AATCTCAAAGAGCTTCAG
EST: gi|78081870|gb|DV510282.1|DV510282
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|89757241|gb|DY686923.1|DY686923
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
EST: gi|74244253|gb|DT652167.1|DT652167
EST:     GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAA                         GCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA
genomic: GAGTATAGAAAACTAAAGGCGAAGGTCGAGACAATACAAAAATGTCAAAAgtaatttgta ... tgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtaatatgccctgttgaagataaatatgaccaatacttttgtgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCAACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG
                                       cttttgt  CT-rich tract
                 ttgaagataaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgtagtgattagttgctgaaaaaatgtaatatgccctgttgaagataaatatgaccaatacttttgtgtcctgcagGCACCTCATGGGAGAGGATCTTGAAACGTTGAATCTCAAAGAGCTTCAGCAACTAGAGCAGCAGCTGGAGAGTTCACTGAAACATATCAGAACCAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA