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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcggttcgaactttgtttttctgttatgaaagtaatataagtggggtcatcctcttataaaaaaaaacctactcatggaaagaggttacgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCTCCGTCGACCATGGGCGGCGAGGGATGCGATAACATGACGATGATCCTGG

Basic information

species Zea mays
transcript GRMZM2G019812_T01
intron # 9
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|18180597|gb|BM381807.1|BM381807
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
EST: gi|60351922|gb|DN218895.1|DN218895
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
EST: gi|148956071|gb|EC901822.2|EC901822
EST:     GCATGTCAAGCCAGCAGTTGGTGGATTTCATCCGCGAGCATATAGACACA                         GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
EST: gi|14244484|gb|BG842495.2|BG842495
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
EST: gi|3157148|gb|AA979770.1|AA979770
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
EST: gi|18964420|gb|BM660995.1|BM660995
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         GAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCT
EST: gi|9742960|gb|BE519108.1|BE519108
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         T
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcag-
EST: gi|9742960|gb|BE519108.1|BE519108
EST:     GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACA                         T
genomic: GCATGTCAAGCCAGCAGTTGGTCGATTTCATCCGCGAGCATATAGACACAgtaagtacca ... cgaagtgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtcatcctcttataaaaaaaaacctactcatggaaagaggttacgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCTCCGTCGACCATGGGCGGCGAGGGATGCGATAACATGACGATGATCCTGG
           ttataaaaaaaaacct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcggttcgaactttgtttttctgttatgaaagtaatataagtggggtcatcctcttataaaaaaaaacctactcatggaaagaggttacgaagtgcagGAGGAAAGCCTCTCGGCAGTATGCGAGAGAGTGCTCGATAGATGCCTGGCTCCGTCGACCATGGGCGGCGAGGGATGCGATAACATGACGATGATCCTGG

- - - - - - - - - ttttctg
- - - - - - - - - - - - - - -gaaagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa