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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagattggtgtttaactgcttgctttgtagggtttttttacccatgcatttgtttatgttgcttacacttgaaagcaattcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGATTGCAGAACGTTGAGAAGGCTGTTTGAACATGATGGCAGTAGCAATCTG

Basic information

species Zea mays
transcript GRMZM2G110143_T01
intron # 7
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|149005363|gb|EE039915.2|EE039915
EST:     TTCCATCACCGAAGGGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATTTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|9953659|gb|BE640242.1|BE640242
EST:     CGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|4612952|gb|AI603791.1|AI603791
EST:     CTCCATCNCCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|78076982|gb|DV505416.1|DV505416
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|4886171|gb|AI677291.1|AI677291
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|4610219|gb|AI601058.1|AI601058
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|4612935|gb|AI603774.1|AI603774
EST:     CTCCATCCCCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|71325766|gb|DR799564.1|DR799564
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|89757945|gb|DY687313.1|DY687313
EST:     TTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATTTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|50335676|gb|CO530802.1|CO530802
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|31558120|gb|CD527332.1|CD527332
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|74237053|gb|DT644967.1|DT644967
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|50328941|gb|CO524067.1|CO524067
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|211440858|gb|FL253847.1|FL253847
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|29543368|gb|CB603764.1|CB603764
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|74241217|gb|DT649131.1|DT649131
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|29543688|gb|CB604068.1|CB604068
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|211537739|gb|FL446830.1|FL446830
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|5608416|gb|AI901993.1|AI901993
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|4610220|gb|AI601059.1|AI601059
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|30306409|gb|CD001082.1|CD001082
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|28982754|gb|BQ538326.2|BQ538326
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|74243433|gb|DT651347.1|DT651347
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|89247003|gb|DY618789.1|DY618789
EST:     TTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|30307255|gb|CD001928.1|CD001928
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|76290039|gb|DV029607.1|DV029607
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|18177716|gb|BM378926.1|BM378926
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
EST: gi|86474392|gb|DY240762.1|DY240762
EST:     CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAG                         GAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA
genomic: CTCCATCACCGAAGCGTGCAAGCTCCCGCAGCCCAGGCAGCGATAGCAAGgttagattgg ... ttcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttacccatgcatttgtttatgttgcttacacttgaaagcaattcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGATTGCAGAACGTTGAGAAGGCTGTTTGAACATGATGGCAGTAGCAATCTG
                          tgcttac  putative branch site (score: 2)
              atttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagattggtgtttaactgcttgctttgtagggtttttttacccatgcatttgtttatgttgcttacacttgaaagcaattcatgtcagGAATAAAGCTTGTTGATCTGGTGATGCTTAAAGAGCAGTCTTCCCATGGGATTGCAGAACGTTGAGAAGGCTGTTTGAACATGATGGCAGTAGCAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT