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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgacggattttgggattgtctagtagatgttttcaagggtttgctcaccgattgtttggtgtggctactgatttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATGCTCCGCCAGTACCCAAGTGTGAGACCAGG

Basic information

species Zea mays
transcript GRMZM2G113592_T01
intron # 2
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|211227313|gb|FL251474.1|FL251474
EST:     GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCG                         GGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
genomic: GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCGgtgagtcgac ... ttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
EST: gi|148978947|gb|EE026414.2|EE026414
EST:     GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCG                         GGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
genomic: GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCGgtgagtcgac ... ttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
EST: gi|148967855|gb|EE019150.2|EE019150
EST:     GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCG                         GGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
genomic: GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCGgtgagtcgac ... ttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
EST: gi|89759256|gb|DY688127.1|DY688127
EST:     GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCG                         GGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
genomic: GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCGgtgagtcgac ... ttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
EST: gi|211227314|gb|FL251475.1|FL251475
EST:     GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCG                         GGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
genomic: GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCGgtgagtcgac ... ttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
EST: gi|211227311|gb|FL251472.1|FL251472
EST:     GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCG                         GGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
genomic: GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCGgtgagtcgac ... ttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
EST: gi|91051679|gb|EB162097.1|EB162097
EST:     GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCG                         GGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG
genomic: GCTCGAGTACAAGCCCCCGCTGGAGAAGCGCAAATTGCCGGCCTACACCGgtgagtcgac ... ttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcaagggtttgctcaccgattgtttggtgtggctactgatttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATGCTCCGCCAGTACCCAAGTGTGAGACCAGG
                                      tactgat  putative branch site (score: 2)
                       attgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgacggattttgggattgtctagtagatgttttcaagggtttgctcaccgattgtttggtgtggctactgatttggatgcagGGATGGCACAATTTGTGTCGCACTTTGCTGAGCCCGAGGATCCAGAGTATGCTCCGCCAGTACCCAAGTGTGAGACCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT