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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgcatagtgttgtagtactactgatttttaaaattacctgggtttattgacaatgtaggaggatttacactgttttttttccctttccggacgtagGCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAATGGCATGACGATCAGCAGGGTTCGTAATGGATCCATCCTTCATCGCTTC

Basic information

species Zea mays
transcript GRMZM2G002361_T01
intron # 1
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|149108582|gb|EE189724.2|EE189724
EST:     ATGCTCCCCGAGTGGATGGTCGATGCCCCACCCCACCTCGCCACCGACTG                         GCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAA
genomic: ATGCTCCCCGAGTGGATGGTCGATGCCCCACCCCACCTCGCCACCGACTGgtccgtcctc ... ccggacgtagGCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAA
EST: gi|71314104|gb|DR793668.1|DR793668
EST:     ATGCTCCCCGAGTGGATGGTCGATGCCCCACCCCACCTCGCCACCGACTG                         GCATGTGTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAA
genomic: ATGCTCCCCGAGTGGATGGTCGATGCCCCACCCCACCTCGCCACCGACTGgtccgtcctc ... ccggacgtagGCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAA
EST: gi|50332227|gb|CO527353.1|CO527353
EST:     ATGCTCCCCGAGTGGATGGTCGATGCCCCACCCCACCTCGCCACCGACTG                         GCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAA
genomic: ATGCTCCCCGAGTGGATGGTCGATGCCCCACCCCACCTCGCCACCGACTGgtccgtcctc ... ccggacgtagGCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttattgacaatgtaggaggatttacactgttttttttccctttccggacgtagGCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAATGGCATGACGATCAGCAGGGTTCGTAATGGATCCATCCTTCATCGCTTC
   tattgac  putative branch site (score: 2)
                      tttacactgttttttt  putative PPT
                             tgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgcatagtgttgtagtactactgatttttaaaattacctgggtttattgacaatgtaggaggatttacactgttttttttccctttccggacgtagGCATGTTTTTGCCCGACCTTCTGGCAAACGATGTTTGGTTGTGTCATCCAATGGCATGACGATCAGCAGGGTTCGTAATGGATCCATCCTTCATCGCTTC

-ctttgca
- - - - - -tgttgta
- - - - - - - - - - -ctactga
- - - - - - - - - - - - - - - - - - - tacctgg