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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgtatgtctgagctgtgtgatttatctgtattgatgaaagcataagcatcattagtgaggatgcatatgctaacttatatctttccaatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTGTTCGCAGAGGAGGAAACGCTGCACATGGCCCGGCACAGATTTTCAGTTT

Basic information

species Zea mays
transcript GRMZM2G048210_T02
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|148972548|gb|EE023511.2|EE023511
EST:     CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAG                         TTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
genomic: CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAGgtaagaccag ... aatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
EST: gi|149083839|gb|EE173214.2|EE173214
EST:     CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAG                         TTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
genomic: CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAGgtaagaccag ... aatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
EST: gi|89247678|gb|DY619464.1|DY619464
EST:     CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAG                         TTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
genomic: CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAGgtaagaccag ... aatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
EST: gi|71311036|gb|DR791825.1|DR791825
EST:     CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAG                         TTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
genomic: CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAGgtaagaccag ... aatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
EST: gi|76282773|gb|DV022341.1|DV022341
EST:     CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAG                         TTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
genomic: CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAGgtaagaccag ... aatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
EST: gi|148970105|gb|EE021043.2|EE021043
EST:     CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAG                         TTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
genomic: CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAGgtaagaccag ... aatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
EST: gi|149112504|gb|EE191352.2|EE191352
EST:     CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAG                         TTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG
genomic: CTTGGCGGCGCTCTCGCCGAGCCCCCGGCCTGCGGCCAAGGCGGCACCAGgtaagaccag ... aatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagcatcattagtgaggatgcatatgctaacttatatctttccaatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTGTTCGCAGAGGAGGAAACGCTGCACATGGCCCGGCACAGATTTTCAGTTT
                          tgctaac  putative branch site (score: 1)
                                      tctttcca  putative PPT
                             taacttatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgtatgtctgagctgtgtgatttatctgtattgatgaaagcataagcatcattagtgaggatgcatatgctaacttatatctttccaatggatcagTTCGATCAAATTCACGTGCTTCGAGCTCCAGGAAGGAAGATTCTGTACCTGTTCGCAGAGGAGGAAACGCTGCACATGGCCCGGCACAGATTTTCAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA