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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgccccggacgagatcccgtatcatttcgttgcttgttttgcgggatcgggctgttgggccgaatccattttgatggtgtccgtctagatcta...

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 5'ss of exon 2
-------------GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcg---ccccggacgagatcccgtatcatttcgttgcttgttttgcggg---atcgggctgttgggccgaatccattttgatggtgtccgtctagatcta
             || |||||| ||||||| ||||| || || || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||   |    || | |  |    |||| ||||||  ||| | |  ||||  |   || |||  ||| |   | ||  | ||   ||  |  ||   || ||  
TGTGTGTGTGCAGGCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatgagatcctgtagtacgatccgtttcattt--ttgttcggcttgcttgtctattggggggtttg-tggcattgactt--gtgccggtcggtgaggtca-

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 3
GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcg---ccccggacgagatcccgtatcatttcgttgcttgttttgcggg---atcgggctgttgggccgaatccattttgatggtgtccgtctagatcta
|| |||||| ||||||| ||||| || || || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||   |    || | |  |    |||| ||||||  ||| | |  ||||  |   || |||  ||| |   | ||  | ||   ||  |  ||   || ||  
GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatgagatcctgtagtacgatccgtttcattt--ttgttcggcttgcttgtctattggggggtttg-tggcattgactt--gtgccggtcggtgaggtca-
















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|32829264|gb|CD968942.1|CD968942
EST:     TCATCGGCTCGTACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAATTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|32787712|gb|CD936614.1|CD936614
EST:     TCATCGG-TCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|32829447|gb|CD969125.1|CD969125
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     CTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: CTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|32797525|gb|CD949761.1|CD949761
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTAGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|32914071|gb|CF018883.1|CF018883
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|32796729|gb|CD948965.1|CD948965
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     GCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: GCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|32799379|gb|CD951615.1|CD951615
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|32798044|gb|CD950280.1|CD950280
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|211283078|gb|FL322113.1|FL322113
EST:     TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgc ... ttacgttcagGTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcgccccggacgagatcccgtatcatttcgttgcttgttttgcgggatcgggctgttgggccgaatccattttgatggtgtccgtctagatcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC