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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgttgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactgatctgctgttctcgcctcgcag

Basic information

species Zea mays
transcript GRMZM2G003424_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g21160.1 (Oryza sativa), 5'ss of exon 3
TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgc----attgcgttgcgaattcatcctt-cgcttccagcaacggcaatggcgtccgtgca----tgcacgcatgcagttgcttgggttaactgatctgct-gttctcgcctcgcag-------------------------------
||||||| ||| |||||||||||||||||||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||||||||||||| | |     |  |||    ||||  |    | |     |    | |  ||  ||  |     |    |    | || |   | | | | ||  |    ||||| |    |  |  |||                                
TGAAGCTGATCTTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCCTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgtacgttcgaaacgcggcttgaatgaagaaatgcatgcgcgattatgttaagcgctccaaattagtagtagtagtatactactacgttgcttgtcacgactgctagccaccaacctgcatgcatgtgaatttgttgttcgtcgctcctcag

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g21140.1 (Oryza sativa), 5'ss of exon 3
TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgc----attgcgttgcga-attcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgc-agttgcttgggttaactgatctgctgttctcgcctcgcag
||||||| ||| ||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||||||||||||||| ||    |   || | ||   ||     | ||| ||    ||| ||||  |  ||||||||||||    | |  |||||||    ||| |  | | |    |||  || ||||
TGAAGCTGATCTTGGCCAAGGGCAATCCGCATTTCATCTGCGACGCCCGCGTGCTCGTCAAGCCTTACAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcacgcttggaacacgctccggcgttttaattccgcatctttaaactgcaactgtatccgtgcatgcagttttcctggttgctta---taattttttttcca--ctcatcttgcag

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G01350.1 (Glycine max), 5'ss of exon 3
TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgttgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactg--atctgctgttctcgcctcgcag
||||||| || ||  | || || ||||| || ||  | || || ||||| ||||| || ||||| || |||||||||||||| ||||| ||||||||||||||  |  | | ||      | ||  |    ||        |  | |  | |  ||   |    | |||   |  ||   |||   ||  || ||| |              
TGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcaccccct-ctttctactcttatgttaactttttgtttttgttattcccttgagtttgt-tttgaatgtgctcactattgtttcttgtgatttgcag--------------

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G01350.2 (Glycine max), 5'ss of exon 3
------TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgttgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactg--atctgctgttctcgcctcgcag
      ||||||| || ||  | || || ||||| || ||  | || || ||||| ||||| || ||||| || |||||||||||||| ||||| ||||||||||||||  |  | | ||      | ||  |    ||        |  | |  | |  ||   |    | |||   |  ||   |||   ||  || ||| |              
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccct-ctttctactcttatgttaactttttgtttttgttattcccttgagtttgt-tttgaatgtgctcactattgtttcttgtgatttgcag--------------

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G01340.1 (Glycine max), 5'ss of exon 4
------TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgttgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactgatctgctgttctcgcctcgcag
      ||||||| || ||  | || || ||||| || ||  | || || ||||| ||||| || ||||| || |||||||||||||| ||||| ||||||||||||||  |  |   || | | |      ||  |||             |     || ||  |            |||  || | | |||    || |  |   |  | ||||
AGACCGTGAAGCTTATTCTATCTAAAGGAAACCCTCATTTTGTGTGTGATGCACGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcaccccct--ctttctactcttatgttatcttttttttgtttttgttattcccttgagtttgtt-------ttgaatgtgctcacta--ttgtttcttgtgatttgcag

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G35990.1 (Glycine max), 5'ss of exon 7
TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgt-----tgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactgatctgctgttctc---gcctcgcag
||||||| || ||  |||| || || || || ||  | || || || || ||||| || ||||| || |||||||||||||| ||||| ||||||||||||||  ||   | |     | |   |   |  |    ||          |  |    |   ||  |     | ||   ||  || |  |  |     || ||||      |  | ||||
TGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAGTACAGgcacccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtttattttgaatgtcctcattgatgtttcttgtgatttgcag

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G35980.1 (Glycine max), 5'ss of exon 4
------TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgt-----tgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactgatctgctgttctc---gcctcgcag
      ||||||| || ||  |||| || || || || ||  | || || || || ||||| || ||||| || |||||||||||||| ||||| ||||||||||||||  ||   | |     | |   |   |  |    ||          |  |    |   ||  |     | ||   ||  || |  |  |     || ||||      |  | ||||
AGACTGTGAAGCTTATTCTATCCAAAGGAAATCCTCATTTTGTGTGTGATGCTCGAGTGCTTGTTAAGCCTTACAAGGAGAAGGGCAAAGTCCCAGACAAgtacaggcacccaccccctctttctactcttatgttatcttttttttttcttttcttttttctttttggttattgtcttgagtttattttgaatgtcctcattgatgtttcttgtgatttgcag

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0158g00370.t01 (Vitis vinifera), 5'ss of exon 4
------TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgttgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgca-cgcatgcagttgcttgggttaactgatctgctgttctcgcctcgcag
      ||||||||||  |||| || || ||||| || ||  | || || || || || || || ||||| ||||||||||||||||| ||||| ||||||||||||||                |   | || | || ||   ||  ||  |||  |   ||  |||| |      ||| |||   | ||| |  | ||  |||   |        
AGACAGTGAAGCTCATTTTGGCTAAAGGGAACCCTCATTTTGTTTGTGATGCTCGGGTTCTGGTTAAGCCCTATAAGGAGAAGGGCAAAGTCCCGGACAAgtacaggcac---------------tctcttctgctctccctctaaatgccttggtttttttg-gtgcatcttgcagagtagctgatggtaatt--tttg--gtttcag--------

upper sequence: GRMZM2G003424_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 5'ss of exon 3
------TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgttgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactgatctgctgttctcgcctcgcag
      ||||||||||  | || || || ||||| || ||| | || ||  | || |||||||| ||||| |||||||||||||| || ||||| || ||||| ||||||    |   ||  |   |  |  || |  |     |    |       | | |  ||  | |    || ||| |  | || |   || ||| |              
AGACTGTGAAGCTCATTTTAGCTAAAGGGAACCCCCATTTCGTATGTGATTCGCGTGTGCTCGTAAAGCCCTATAAGGAGAAGGGAAAAGTCCCGGAAAAgtataggcattttctctcttttgtgcttttgttttgtgtgtgttactcac-------ttcatatattgatgttaaca-ttgtt--gattgaacaat-tgcag--------------

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|26456157|gb|CA827740.1|CA827740
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|211500619|gb|FL214005.1|FL214005
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|211500615|gb|FL214001.1|FL214001
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|211500618|gb|FL214004.1|FL214004
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|71757084|gb|DR955021.1|DR955021
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|28930856|gb|CB334217.1|CB334217
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|149015221|gb|EE045006.2|EE045006
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|9254329|gb|BE344797.1|BE344797
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|87156061|gb|DY400850.1|DY400850
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|29945367|gb|CB815603.1|CB815603
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|211500616|gb|FL214002.1|FL214002
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|74236816|gb|DT644730.1|DT644730
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCCAGGTCCCCGACAAGTACAG                         GAAGCCGCAGCAAGGGGACTTCTCCGGCTGCACCACGCCCCACTGGGGGGC
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCC-ACTGGCGGGC
EST: gi|211500621|gb|FL214007.1|FL214007
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|211500620|gb|FL214006.1|FL214006
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
EST: gi|148951391|gb|EC897107.2|EC897107
EST:     GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAG                         GAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT
genomic: GTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattg ... cgcctcgcagGAAGCAGCAGCAAGGGGACTTCTCCGGCTGCACGACGCCCACTGGCGGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGCTCATCCTGGCCAAGGGCAACCCGCACTTCATCTGCGACGCACGCGTGCTCGTCAAGCCGTATAAGGAGAAGGGCAAGGTCCCCGACAAGTACAGgcatgcattgcgttgcgaattcatccttcgcttccagcaacggcaatggcgtccgtgcatgcacgcatgcagttgcttgggttaactgatctgctgttctcgcctcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA