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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttgtgtcctttgttaactttagtgtaacgatgcataagttggttcactttatatttccattgtcattaccagctaactccttccattctctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC

Basic information

species Zea mays
transcript GRMZM2G061620_T02
intron # 4
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|211500818|gb|FL228127.1|FL228127
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|76012358|gb|DT939528.1|DT939528
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|5296098|gb|AI782973.1|AI782973
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|7216451|gb|AW562573.1|AW562573
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211500819|gb|FL228128.1|FL228128
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|4314922|gb|AI444722.2|AI444722
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211500823|gb|FL228132.1|FL228132
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|211500820|gb|FL228129.1|FL228129
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCWGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|101401583|gb|EB822467.1|EB822467
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|32915276|gb|CF020088.1|CF020088
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCAAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|76280698|gb|DV020266.1|DV020266
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
EST: gi|4681058|gb|AI629728.1|AI629728
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCG
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCG
EST: gi|211500822|gb|FL228131.1|FL228131
EST:     CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTAT                         TGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC
genomic: CCTGCTACTCCACCTCAAACGTCAGCAGCCCCAGATGCACCGGCACCTATgtgagcttca ... tctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactttatatttccattgtcattaccagctaactccttccattctctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC
                           agctaac  putative branch site (score: 2)
                                 ctccttccattctct  CT-rich tract
     ttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttgtgtcctttgttaactttagtgtaacgatgcataagttggttcactttatatttccattgtcattaccagctaactccttccattctctgaattagTGTACCTGTCAGTGCACCGGCTGCAACTGCTACAGCCTCAGCAGCTCCTGCTGTTGCTGTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT