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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtattttgttacttattctttgattgtgtctatgagctggtggcatcgtactcatccattgtacatacacgtttcatgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG

Basic information

species Zea mays
transcript GRMZM2G055520_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055520_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g06070.1 (Oryza sativa), 3'ss of exon 9
gtatgtgtat-tttgttacttattctttgattgtgtcta-----------------tgagctggtggcatcgtactcatccattgtacata------cacgtttcatgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG
||||||| || |||  ||||  ||||   ||  | | ||                 | ||||||||     || ||| ||| || ||| ||      |  |||||||| | |||||||| || ||||| ||||| ||||| || ||||| ||||||||||||||| |    ||||||||||||||||||
gtatgtggatattttctactgtttctgctatcttctttaaaaaaagaaaaaaaatgttagctggtgtagaagtgctcttccgttttacttatcttatcttgtttcatggtccagGTAAGGGGGGATGACAAAGATGATCCCACGACATATCTTGTCACATTTGATGAC---GATGGTGCAAAATATTTG
















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|67028367|gb|CO457116.1|CO457116
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|211117417|gb|FL123104.1|FL123104
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|6445442|gb|AW179360.1|AW179360
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|78026209|gb|DV494596.1|DV494596
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|51592768|gb|CV071914.1|CV071914
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|6445422|gb|AW179490.1|AW179490
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|71432829|gb|DR813879.1|DR813879
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|76286686|gb|DV026254.1|DV026254
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
EST: gi|101389744|gb|EB816806.1|EB816806
EST:     ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAA                         GTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT
genomic: ATGAAAACGATGACATCCAGTATTCCTGGCTAAGAGAATATCACTGGGAAgtatgtgtat ... catgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtattttgttacttattctttgattgtgtctatgagctggtggcatcgtactcatccattgtacatacacgtttcatgattcagGTAAGAGGAGATGATAAAGACGATCCTACAACATACCTTGTCACATTTGATAAGAAGGATGGTGCAAAATATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG