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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttccaacattcttgactgtatagtgtctggcacattgtcataatttcataattatttgttttaataaatagtaattgcttattttcttttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATGGAAGCTAATAGATTTTATGATGCTGTCAGTTGTCTGATGTCTTATATG

Basic information

species Zea mays
transcript GRMZM2G023798_T01
intron # 10
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|23199794|gb|BU582359.1|BU582359
EST:     CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAG                         GCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
genomic: CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcag ... tttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
EST: gi|32837111|gb|CD976789.1|CD976789
EST:     CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAG                         GCCTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
genomic: CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcag ... tttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
EST: gi|18659473|gb|BM500356.1|BM500356
EST:     CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAG                         GCCTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
genomic: CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcag ... tttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
EST: gi|61118731|gb|DN559692.1|DN559692
EST:     CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAG                         GCCTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
genomic: CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcag ... tttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
EST: gi|5566676|gb|AI881587.1|AI881587
EST:     CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAG                         GCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
genomic: CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcag ... tttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
EST: gi|87156285|gb|DY401074.1|DY401074
EST:     CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAG                         GCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
genomic: CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcag ... tttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
EST: gi|26560142|gb|CA832377.1|CA832377
EST:     CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAG                         GCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG
genomic: CTGCTGATCATGGTTGGCCTATATCTGATTGCACTGCTGAAGGACTAAAGgtgaatgcag ... tttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcataattatttgttttaataaatagtaattgcttattttcttttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATGGAAGCTAATAGATTTTATGATGCTGTCAGTTGTCTGATGTCTTATATG
                ttttaat  putative branch site (score: 3)
                                ttgcttattttctttt  putative PPT
     ataattatttgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttccaacattcttgactgtatagtgtctggcacattgtcataatttcataattatttgttttaataaatagtaattgcttattttcttttactccagGCTTCATTATTGTTATCAAGGATCTCTCCCAAAATTGTTGGTGAACCGATGGAAGCTAATAGATTTTATGATGCTGTCAGTTGTCTGATGTCTTATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG