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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattcaatttctttttttttccttatccgtgtcataagtggaaactccacttaaatgatgtacatttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG

Basic information

species Zea mays
transcript GRMZM2G090647_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090647_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g37832.1 (Oryza sativa), 3'ss of exon 5
gta-agtattcaatttctttttttttccttatccgtgtcataagtggaaa-------ctccacttaaatgatgtacatttctc-ctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
||   || || |||||  || |  |  ||||||| || |||||   |||        ||  | ||  | |  |||  | | |   |||||||||||  | ||||||||  |||| |||| ||||||||||||||||||
gtgtggtttttaattttcttctcgt--cttatccatgccataataagaagatatcagctgtaatttgaggtggtatttgtttgattagGAATGGGAGCTGGCAGAGAATTTGCAGGGAGTTCTTGAGTACCAAACAAG
















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|5686889|gb|AI939803.1|AI939803
EST:     GATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: GATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|166442029|gb|EG095433.1|EG095433
EST:     CTTTTCCGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: CTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|71770109|gb|DR968046.1|DR968046
EST:     ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|8368443|gb|BE051388.1|BE051388
EST:     ATAGAGAAGGTATTGACTTTTCCGATGCTCAAAACATGCAGCCAGTGCAC                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|30705964|gb|CD058985.1|CD058985
EST:     ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|76918843|gb|DV167481.1|DV167481
EST:     ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|5018209|gb|AI714402.1|AI714402
EST:     ATAGAGAAGGTATTG-CTTTTCCGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|211242536|gb|FL481660.1|FL481660
EST:     ATAGAGAAGGTATTGACTTTTCCGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|211164192|gb|FL363087.1|FL363087
EST:     ATAGAGAAGGTATTGACTTTTCCGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAG-AGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
EST: gi|60336843|gb|DN203816.1|DN203816
EST:     ATAGAGAAGGTATTGACTTTTCCGATGCTCAAAACATGCAGCCAGTGCAG                         GAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
genomic: ATAGAGAAGGTATTGACTTTTCTGATGCTCAAAACATGCAGCCAGTGCAGgtaagtattc ... tttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttatccgtgtcataagtggaaactccacttaaatgatgtacatttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG
                                           catttctcct  CT-rich tract
                               ttaaatgat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattcaatttctttttttttccttatccgtgtcataagtggaaactccacttaaatgatgtacatttctcctagGAATGGGAATTAGCAGAGAACCTGCAAGGAGCTCTTGAGTACCAAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT