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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacgttaattcgtgaatacaggataagcttagtcagttcttatattagaaaccagaacgtattagcttcaatggcatgacatggctgttgtttttttttcttctgcag

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 3
ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacgttaattcgtgaatacaggataagcttagtcagttcttatattagaaaccagaacgtattagcttcaatggcatgacatggctgttgtttttttttcttctgcag
|||||| || ||||||||||||||| || |||| ||||||||||| || ||||||||||| ||||||||||||||||||||     ||   ||   | | |  |||||| ||| |  |     ||| || |||   |||  ||||||||||   |  |||      | |    ||  |   | ||||||||
ACGGCCAGGCCAGAGCAGAATAACCACCCCAAGAAAGGAGACTGACACTTGCAAAATTCTTTCAGGGACACATGAAGgtat--ggtgtc--tttcaggacatgggataaacttggaaaaaa--tatttttgaatttaga--gtattagctt--gtctcatattcacgatagcattgatgggttttctgcag
















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|211106359|gb|FL258168.1|FL258168
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|148952455|gb|EC898280.2|EC898280
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|148950436|gb|EC896004.2|EC896004
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149088416|gb|EE177517.2|EE177517
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAAC
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAAC
EST: gi|149096924|gb|EE182722.2|EE182722
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|211106357|gb|FL258166.1|FL258166
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCSAATTCTTTGTTATTGTCCCAAACACAGATTCA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTT-GTTATTGTCCCAAACACAGAT-CA
EST: gi|149088025|gb|EE177228.2|EE177228
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149089246|gb|EE178450.2|EE178450
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149106625|gb|EE188518.2|EE188518
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|148950790|gb|EC896395.2|EC896395
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|148951094|gb|EC896759.2|EC896759
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149111173|gb|EE294669.2|EE294669
EST:     CACAAGGAAGGAGACTGATACATGCCAAATTCTGTCAAGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGA
EST: gi|211106358|gb|FL258167.1|FL258167
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149084565|gb|EE174034.2|EE174034
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|76281790|gb|DV021358.1|DV021358
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149067437|gb|EE287007.2|EE287007
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|148936477|gb|EC880584.2|EC880584
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149098825|gb|EE184838.2|EE184838
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|211106354|gb|FL258163.1|FL258163
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTYTGTCAGGVACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGT
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGT
EST: gi|76934911|gb|DV174083.1|DV174083
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|211106355|gb|FL258164.1|FL258164
EST:     CACAAGAAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGTACGCCAATTCTTGT
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGT
EST: gi|211106349|gb|FL258158.1|FL258158
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|148957149|gb|EC903140.2|EC903140
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|211106350|gb|FL258159.1|FL258159
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|149071022|gb|EE159425.2|EE159425
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
EST: gi|211106353|gb|FL258162.1|FL258162
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTNGAACGCCAATTCTTGTTATTGTCC-AAACACAGATCAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAA
EST: gi|149036977|gb|EE155215.2|EE155215
EST:     CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAG                         GGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA
genomic: CACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacg ... tcttctgcagGGGTGACTACTGGAACGCCAATTCTTGTTATTGTCCCAAACACAGATCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGCCCGGACAGAGCAGAATAACCTCCACAAGGAAGGAGACTGATACATGCAAAATTCTGTCAGGGACACATGAAGgtatccaacgttaattcgtgaatacaggataagcttagtcagttcttatattagaaaccagaacgtattagcttcaatggcatgacatggctgttgtttttttttcttctgcag

- - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - -  AGGAGA