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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctcacttgccccccaccggccattggacccaactgcctgtcgcgctaactttttcgtgtatatccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCCGGTGGTGGCAAGCAAAAGAAGAAG

Basic information

species Zea mays
transcript GRMZM2G084868_T03
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|211114494|gb|FL397754.1|FL397754
EST:     CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
genomic: CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
EST: gi|211301114|gb|FL396192.1|FL396192
EST:     CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGGACAA-GCCCCGCCGCTCGTCGTCGAAGCCGGCCAAGTC
genomic: CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGC-CGTCGTCGAAGCCGGCCAAGTC
EST: gi|211439670|gb|FK960515.1|FK960515
EST:     CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
genomic: CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
EST: gi|211069269|gb|FL419942.1|FL419942
EST:     CTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGG
genomic: CTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGG
EST: gi|9952372|gb|BE638955.1|BE638955
EST:     AGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
genomic: AGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
EST: gi|211459128|gb|FL410726.1|FL410726
EST:     CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
genomic: CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCC
EST: gi|211066393|gb|FK960539.1|FK960539
EST:     CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGGTC
genomic: CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAG-TC
EST: gi|211381879|gb|FL378662.1|FL378662
EST:     CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATG                         GCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCG
genomic: CCCCTCCCCTTCGCTTCCTTCCCTAGCGCCGACGCCCACCAGACGAGATGgtgcgctcac ... atccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggccattggacccaactgcctgtcgcgctaactttttcgtgtatatccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCCGGTGGTGGCAAGCAAAAGAAGAAG
                          cgctaac  putative branch site (score: 2)
                                            tatcctt  putative PPT
                             taacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctcacttgccccccaccggccattggacccaactgcctgtcgcgctaactttttcgtgtatatccttgcagGCCCCGAAGAAGGACAAGGCCCCGCCGCCGTCGTCGAAGCCGGCCAAGTCCGGTGGTGGCAAGCAAAAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG