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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attccaataacatgccttgtgaatttaatggtgtcctgtcgatgcattttttccatactataatttgaagtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG

Basic information

species Zea mays
transcript GRMZM2G081653_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 3
--attccaataacatgccttgtgaatttaatggtgtcctgtcgatgcattttttccatactataatttgaa-gtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG
   | |  | |||||   |  |  | || |   |||   |   ||   |||| ||||||   |||  ||||  ||  |   | | |||||| | ||||  ||||||||||||||| | ||||| || || ||||| ||||||||||||||||| || |||||
ctctgcagaaaacatcattgttttactttaccatgtaaagctaatc--ttttgtccatatggtaagctgaatatgaattggtgggattttgaaatttt-gtagGTACAAAACTTAATTGAGAAGCCTCAATATGACCATTTGCCACTAATTGAAGCGAGCAG
















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|89764107|gb|DY691035.1|DY691035
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTGATTGAG
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
EST: gi|78075488|gb|DV503922.1|DV503922
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAAACT-ACTCGAGAAACCACAGTATGATCATT
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAA-CTTACTCGAGAAACCACAGTATGATCATT
EST: gi|71445741|gb|DR826791.1|DR826791
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAAC-ACAGTATGATCAT
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCAT
EST: gi|149090139|gb|EE179439.2|EE179439
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
EST: gi|76911678|gb|DV164374.1|DV164374
EST:     TCAAAGTCTAAAGAAACAGCCTCCTGAAAAGC-AAGAACTGTTGTCTAAA                         GTACAAAACCTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
genomic: TCAAAGTCTAAAGAAGCAGCCTCCTGAAA-GCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
EST: gi|148973267|gb|EE024347.2|EE024347
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAG
EST: gi|149014320|gb|EE043899.2|EE043899
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAAACACAGTATGATCATTTGCCACT
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACT
EST: gi|71421265|gb|DR805363.1|DR805363
EST:     CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAA                         GTACAAAACTTACTCGAGAAACCACAGTATGATCATTTTGCCACTAATTGA
genomic: CTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatcc ... ttttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTT-GCCACTAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttccatactataatttgaagtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG
                                           tatttttt  CT-rich tract
                               aatagcattttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attccaataacatgccttgtgaatttaatggtgtcctgtcgatgcattttttccatactataatttgaagtgcttcaatagcattttgtattttttatagGTACAAAACTTACTCGAGAAACCACAGTATGATCATTTGCCACTAATTGAGGCTAGCAG

- - - - -acatgcc
- - - - - - - - - - - - - - - -tgtcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttc