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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGCGGGTCAACTGCATCAACTGCTGTACTTGTTGGTGATCGTCTCTTCGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggcttcactgtgcttgttctttaaacctcttgttacttttacacgagtcaattgaatttcatctaaaccttctttaatgaaaatagaacatag...

Basic information

species Zea mays
transcript GRMZM2G056572_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056572_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g56450.2 (Oryza sativa), 5'ss of exon 4
CAATGCGGGTCAACTGCATCAACTGCTGTACTTGTTGGTGATCGTCTCTTCGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgta-ccaaggcttcactgtgcttgttctttaaacctcttgttacttttacacgagtcaattgaatttcatctaaaccttctttaatgaaaatagaacatag-
|| || || |||||||||||||| ||||| ||||||||||| |||||||| || ||||| ||||| |||||||||||||||||||||||||  ||||||||||    |   |||||||| |    |||| |     || ||| | |||||  ||  |  |   | || || ||   | |     || |   |    | |   
CAGTGTGGATCAACTGCATCAACCGCTGTCCTTGTTGGTGACCGTCTCTTTGTTGCAAACGTTGGAGACTCTAGGGCTATCATATGCAGGGGGGGAAATGgtaattgacagttcactgtaccatctcttcagcttcctggttgcatttacttgatactttctgactttatatag--catgacacattattttttttcttttt
















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|76016319|gb|DT943489.1|DT943489
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|26558429|gb|CA830664.1|CA830664
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|211036167|gb|FL457683.1|FL457683
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|94472146|gb|EB701104.1|EB701104
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|76016318|gb|DT943488.1|DT943488
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|60354881|gb|DN221854.1|DN221854
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|71448387|gb|DR829437.1|DR829437
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|60351289|gb|DN218262.1|DN218262
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|31406344|gb|CD485076.1|CD485076
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGC
EST: gi|101386844|gb|EB815439.1|EB815439
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|74237808|gb|DT645722.1|DT645722
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|211062962|gb|FL387714.1|FL387714
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGG-AGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|61118718|gb|DN559679.1|DN559679
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|5296366|gb|AI783136.1|AI783136
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|18660188|gb|BM500731.1|BM500731
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|87156931|gb|DY401720.1|DY401720
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|76917080|gb|DV166669.1|DV166669
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|211036166|gb|FL457682.1|FL457682
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|91051774|gb|EB162192.1|EB162192
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAAGG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|149111016|gb|EE294515.2|EE294515
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|5846990|gb|AW000069.1|AW000069
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|76290021|gb|DV029589.1|DV029589
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|60338245|gb|DN205218.1|DN205218
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|149106821|gb|EE188718.2|EE188718
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|211187859|gb|FL425729.1|FL425729
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|60394530|gb|DN227400.1|DN227400
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|60359261|gb|DN226234.1|DN226234
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|22133680|gb|BQ833845.1|BQ833845
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|60357297|gb|DN224270.1|DN224270
EST:     GCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: GCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|211113689|gb|FL397728.1|FL397728
EST:     GTCGCAAATGTTGGTGACTCTAGGGCTATCATATTGCAGGGAAGGAAATG                         G
genomic: GTCGCAAATGTTGGTGACTCTAGGGCTATCATAT-GCAGGGAAGGAAATGgtaccaaggc ... ctttttgcag-
EST: gi|211113689|gb|FL397728.1|FL397728
EST:     GTCGCAAATGTTGGTGACTCTAGGGCTATCATATTGCAGGGAAGGAAATG                         G
genomic: GTCGCAAATGTTGGTGACTCTAGGGCTATCATAT-GCAGGGAAGGAAATGgtaccaaggc ... ctttttgcag-
EST: gi|149111015|gb|EE294514.2|EE294514
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|71762691|gb|DR960628.1|DR960628
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|50323711|gb|CO518837.1|CO518837
EST:     CGTCGCAA-TGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|211209068|gb|FL368391.1|FL368391
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATGGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATG
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATG
EST: gi|76288715|gb|DV028283.1|DV028283
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
EST: gi|76931265|gb|DV172687.1|DV172687
EST:     CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATG                         CTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC
genomic: CGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggc ... ctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGCGGGTCAACTGCATCAACTGCTGTACTTGTTGGTGATCGTCTCTTCGTCGCAAATGTTGGTGACTCTAGGGCTATCATATGCAGGGAAGGAAATGgtaccaaggcttcactgtgcttgttctttaaacctcttgttacttttacacgagtcaattgaatttcatctaaaccttctttaatgaaaatagaacatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA