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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggaagtcgacaaaggaaatacttcacctacattttttttgtacatattaagcctgcttttagttgcatggaatgatagtctttatgtctgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGC

Basic information

species Zea mays
transcript GRMZM2G006130_T06
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 11
-----gtggaagtcgacaaaggaaatacttcacctacattttttttgtacatattaagc-ctgcttttagttgcatggaatgatagtctttatgtctgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGC
      ||| | |  ||||  |   ||||| | ||   |       | |  | || ||  || ||||||| |  ||| | ||||  ||| | | || |||| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| ||||||| |||||| ||||||||||||||||||||
ccccaatggtactgcacaa--gttttacttgaactgtgtggaga--gcaactgttgagttctccttttaggtatatgca-tgatgttctct-tatccgttatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCGGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGACCACTTGACCATCCTGC

upper sequence: GRMZM2G006130_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 11
gtggaagtcgacaaaggaaatacttcacctacatttttttt-gtaca--tatt-aagcctgcttttagttgcatggaatgatagtctttatgtctgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGC
 |  ||   || || | | ||  || || |  ||| | |   | |||  | || ||  ||  |||||| | |||| | ||||| ||| | | ||  ||| ||||||||||||||||| || || ||||||||||| |||||||||||||||||||| ||||||||||| ||||||| |||||| || |||||||||||||||||
ctccaa--tgataaggcacatgtttgacttgaattgtgtggagaacaactgttgaattctcattttaggtacatgca-tgatattctct-tatccattatacagGTAATTACCTCAAGTTTTATAATGCTATAAGGGAGGCCTATCCAGACATTCAAATGATTTCAAATTGTGATGCTTCATCAAGTCCACTTGACCATCCTGC
















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|32923966|gb|CF028778.1|CF028778
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     CAAACATGCCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|18654845|gb|BM499650.1|BM499650
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGGTCTACCGNG                         GNAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|150037294|gb|DY843524.1|DY843524
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTCCAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32924623|gb|CF029435.1|CF029435
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTG                         GTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC
genomic: CAAACATGTCGCAATTGGAAATGAAGATTGCGGGAAAAAGTTCTACCGTGgtaaacttat ... tgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattaagcctgcttttagttgcatggaatgatagtctttatgtctgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGC
             ttttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggaagtcgacaaaggaaatacttcacctacattttttttgtacatattaagcctgcttttagttgcatggaatgatagtctttatgtctgttaaacagGTAATTACCTCAAATTCTACAATGCTATAAGAGAGGCCTATCCAGACATTCAGATGATTTCAAACTGTGATGGTTCATCTAGACCACTTGACCATCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG