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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTGTCCGCCGCCGCCACTCACTACAAGGAGAAATGGGCAACAGCGACGCTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgggctattttcctttcggggtggggtcggggcgatctctctggttcggttcctggtttggtttggtttggtttgatttgattgcgcagcgtgccgatctgatctgagttctgtccttttatggtgttcctttcag

Basic information

species Zea mays
transcript GRMZM2G029001_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029001_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os04g38970.2 (Oryza sativa), 5'ss of exon 1
-------ATCTGTCCGCCGCCGCCACTCACTACAAGGAGAAATGGGCAACAGCGACGCTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgggctattttcctttcggggtggggtcggggcgatctctctggttcggttcctggtttggtttggtttggtttgatttgattgcgcagcgtgccgatctgatctgagttctgtccttttatggtgttcctttcag
         | ||  |  |  | |     || |  || || |||||| ||  ||||||   |||| ||||    || ||||||||||||||| | ||||||||||||||||| |  |    |||| |    ||  | |||  | || |   |     ||  | |||   ||| | || ||  | | | ||| ||   |    | ||  |    || |  |  | | |                       
GCGCCGCCCCGGTGAGAGGTAGACGGGT-CTCCCCGGCGAGATGGGCCACGTCGACGC---ATCGGCCGCC---GCCGCCGCCGCGCGCGACGCGAAGAAGAAGAGGgtaaggg--gttcgttttgcgcggggatttggggggtgggggggtgatctgtgtgattcgatgttggattcgggattgct-gatctgcggg---ggggtttccgcgtgtttcgtatgcag-----------------------
















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|211436608|gb|FL392571.1|FL392571
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211027846|gb|FL309693.1|FL309693
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCG
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCG
EST: gi|211019418|gb|FL374988.1|FL374988
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCNAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|29946923|gb|CB816392.1|CB816392
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211324131|gb|FL423220.1|FL423220
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211153480|gb|FL406041.1|FL406041
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211189289|gb|FL377648.1|FL377648
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211094859|gb|FL386834.1|FL386834
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211225982|gb|FL407836.1|FL407836
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|33771137|gb|CF272798.1|CF272798
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|86471572|gb|DY237942.1|DY237942
EST:     CGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211458924|gb|FL402427.1|FL402427
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|88754727|gb|DY538868.1|DY538868
EST:     CGCGCGCGACTCCAATAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211273339|gb|FL390038.1|FL390038
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|37419995|gb|CF647683.1|CF647683
EST:     CTGCATCGCCCGCATCGGTGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|40286936|gb|CK327328.1|CK327328
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|211111984|gb|FL388628.1|FL388628
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
EST: gi|33770932|gb|CF273226.1|CF273226
EST:     CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGG                         GGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT
genomic: CTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgg ... ttcctttcagGGGAGCCGCTCGGCGGCGAAGCTGAAGCAGAGCAAGCGCGACACACGCCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTGTCCGCCGCCGCCACTCACTACAAGGAGAAATGGGCAACAGCGACGCTGCATCGCCCGCATCGGCGGCCGCCGCGCGCGACTCCAAGAAGAAGAGGgtaagagcgggctattttcctttcggggtggggtcggggcgatctctctggttcggttcctggtttggtttggtttggtttgatttgattgcgcagcgtgccgatctgatctgagttctgtccttttatggtgttcctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG