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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacacaacaccaaatatggttgtcttgctttaagatgtaatgtaaattccacttcatgttccttgaatccttggctgcagttttgagttcacttc...

Basic information

species Zea mays
transcript GRMZM2G145029_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145029_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 5'ss of exon 3
GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacacaacaccaaatatggttgtcttgctttaagatgtaatgtaaattccacttcatgttccttgaatccttggctgcagttttgagttcacttc-------
||||||||||||| |||||| |  ||||  ||||||| |||||||| ||||||||||| |||||||||||||||||||||||| |||| ||||||||   ||| ||   ||| | |||    |||      || || | |    |     |||||  || |  ||  | |    || | ||   ||| |          
GCCATCTCATGGAAAAGATAAATTCTGGTCATGTCCTCCACAGAGCGTTCAGTGTTTTTCTTTTCAACTCCAAATATGAATTGTTACTTCAGgtattgtaacagcatttaatgtagttacaatgc-----aatatatttttggctgtttatcatggaccat--attatggttgacattgttatattcccaatagaatag

upper sequence: GRMZM2G145029_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G47770.1 (Glycine max), 5'ss of exon 3
GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacacaacaccaaatatggttgtcttgctt-taaga-tgtaatgtaaattccacttcatgttccttgaatccttggctgcagttttgagttcacttc
  ||  | ||||| ||||| |||||||  ||| | ||||| |||||||||||||| ||||| |||||||| || ||||| ||||| || ||||||             | || |  ||| |||  |  ||||  |||| | || ||     || |   |      ||   |  |   ||  |  |||  |||| 
-TCACTTGATGGAAAAGATTGAAGCTGAGAATTTGCTGCATAGAGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGGtaagtttcttcgttgatatttttttggcttcatcataagcctgtagtttacatcttgttttaatgtaaacctattgatttcaaaagcatcaagtaaactt-

upper sequence: GRMZM2G145029_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G38550.1 (Glycine max), 5'ss of exon 3
GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacacaacaccaaatatggttgtcttgctttaagatgtaatgtaaattccacttcatgttccttgaatccttggctgcagttttgagttcacttc-
| ||  | ||||| ||||| |||||||  ||| | ||||| |||||||||||||| ||||| |||||||| || ||||| ||||| || ||||||             | || |  ||| | | | | |   |||| | || ||     || |   |      ||   |  |   ||  |  |||  ||||  
GTCACTTGATGGAAAAGATTGAAGCTGAGAATTTGCTGCATAGAGCTTTCAGTGTATTCCTGTTCAACTCAAAGTATGAGTTGCTTCTTCAGgtaagtttcttcattgatatttttttgacct-cataagcctgtagtttacatcttgttttaacgtaaacctatttatttcaaaagcatcaagtaaacttgg

upper sequence: GRMZM2G145029_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 5'ss of exon 3
GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacacaacaccaaat--atggttgtcttgctttaagatgtaatgtaaattccacttcatgttccttgaatccttggctgcagttttgagttcacttc----
| ||||| ||||| ||||| |||||||  ||| | || ||||||||||||||||| ||  | ||||||||||| ||||| ||||| || ||||||||  |  |  | ||  |  || ||      |  |  || | ||     || |||| |  || |   | |  |  ||  |     | || || |||  |     
GTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAGgtattttcttatgatcaccttgattgtgaagacgactctaggtttag----aaatccagt--atctgaatagttttgttcaccattatattcagatcatctagtct

upper sequence: GRMZM2G145029_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 5'ss of exon 3
GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtat-tcacacaacaccaaatatggttgtcttgctttaagatgtaatgtaaattccacttcatgttccttgaatccttggctg--cagttttgagttcacttc--
| ||| | ||||| ||||| ||| |||  ||| | |||||||||||||||||||| || || || ||||| |||| |||||| || || ||||||| |     ||        |  |     || | |       |  |||   | | | |  |||   |||||   |  |||||  ||||  |   || | |    
GTCATTTGATGGAAAAGATTGAATCTGAGAATTTGCTGCACAGAGCTTTCAGTGTATTTCTGTTTAACTCGAAATTTGAATTACTCCTTCAGgtatgtggttgaattttgggaagtgacaagtttcctgcttgcatggtgtgggtgcaaat--atggaacttga---cgaggctgttcagtggttcatttattgtca

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|60355106|gb|DN222079.1|DN222079
EST:     CTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: CTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|148948633|gb|EC898545.2|EC898545
EST:     GAGCTTTCAGTGTTTTCTTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211100857|gb|FL320689.1|FL320689
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211043409|gb|FL322272.1|FL322272
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211523188|gb|FL353428.1|FL353428
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211514701|gb|FL326221.1|FL326221
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|148948634|gb|EC898546.2|EC898546
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|15313313|gb|BI478657.1|BI478657
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|148930170|gb|EC872550.2|EC872550
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|211410145|gb|FL360134.1|FL360134
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
EST: gi|8318714|gb|BE025279.1|BE025279
EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacac ... ttctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAGgtattcacacaacaccaaatatggttgtcttgctttaagatgtaatgtaaattccacttcatgttccttgaatccttggctgcagttttgagttcacttc

- - - - - - - - - - - - - - - - - - - - - GAGCTT