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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agccacttaaataaatggcaaatgaagctattgtttgctgagtgaaaaagaatttgttgtccatctcagtggaacgtgctctaatgtattatgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGTGCATCATGATGCCACTAAAT

Basic information

species Zea mays
transcript GRMZM2G472991_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472991_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 3'ss of exon 2
-----agccacttaaataaatggcaaatgaagctattgtttgctgagtgaaaaagaatttgttgtccatctcagtggaacgtgctctaatgtattatgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGTGCATCATGATGCCACTAAAT
      |  | ||  |  | || |   | |    |||| ||           || ||| |||  |     |  ||   |  | ||  ||| |  |||||||  ||||| ||||||||||| ||||||||| ||||| | |||||||||||  | |||||||||||||| |||||||
caagttggaatttgga--actgactgcttagaacattggttttaagacttgcaacaatatgtcctttgaatgtgttcta-attcttcaatct--tatgaatgaagGCACGGAGGCACATATAAAGTGCTGCGGAATTTGTTGAAGAACAAATTGGTGCATCATGATGCTACTAAAT
















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|211277358|gb|FL192926.1|FL192926
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|20300018|gb|BQ162961.1|BQ162961
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|71429251|gb|DR810301.1|DR810301
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|18384971|gb|BM418170.1|BM418170
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATTGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|93016530|gb|EB642050.1|EB642050
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|91056420|gb|EB166838.1|EB166838
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|89106284|gb|DY576501.1|DY576501
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|78112924|gb|DV531318.1|DV531318
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|20299997|gb|BQ162940.1|BQ162940
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|18384009|gb|BM417209.1|BM417209
EST:     CACGAGA-TGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|18383990|gb|BM417190.1|BM417190
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|76014835|gb|DT942005.1|DT942005
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|18384955|gb|BM418154.1|BM418154
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|76014878|gb|DT942048.1|DT942048
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|22489226|gb|BU049149.1|BU049149
EST:     CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT
EST: gi|78120952|gb|DV539336.1|DV539336
EST:     CACGAGATTGTTCCAGCAAAACTTGTCGACGGGATCGCCAGACTGAA                         GCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAAAACAAGCTAGT
genomic: CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAAgtaagattgt ... atgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagaatttgttgtccatctcagtggaacgtgctctaatgtattatgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGTGCATCATGATGCCACTAAAT
                                 ctctaat  putative branch site (score: 3)
                                    taatgtattatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agccacttaaataaatggcaaatgaagctattgtttgctgagtgaaaaagaatttgttgtccatctcagtggaacgtgctctaatgtattatgaattcagGCATGGAGGCACATACAAAGTGCTGAGGAATCTTTTGAAGAACAAGCTAGTGCATCATGATGCCACTAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT