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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttttataactttctcaaaatcaggaagtcctatattggcttttgaatattatgctaaaatgtgaacataacattgtgacgattaattcttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTCAAGCTTGATAAGGAAAGTAGCTTCAGATAATGTGTTCGTCATCCAG

Basic information

species Zea mays
transcript GRMZM2G026900_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026900_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g33230.1 (Oryza sativa), 3'ss of exon 2
---------aggttttataactttctcaaaatcaggaagtcctatattggcttttgaatattatgctaaaatgtgaacataacattgtgacgattaattcttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTCAAGCTTGATAAGGAAAGTAGCTTCAGATAATGTGTTCGTCATCCAG
         |  |||| ||   | ||||  |  |   |||    | ||| |||   || | ||   |||  ||||||||| |||         |||| ||||||| ||||||||| || || ||| | || || ||||||||||| |||||||||||||||||||  |||||| |  |||||||||  |||||||||||||| |||
tgctttatgatattttctattatgctcatgaaaaaatagtttc-tcttgtcttcctaaaaatagtataagctgtgaacatgaca--------gttaactcttctttcagGGAAGGGCCAACTTTAATTGTCGCGTGTGGCTGGGATACCATATCATATTCAAGCTCAATAAGGCATCTAGCTTCAGGCAATGTGTTCGTCATTCAG
















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|89759150|gb|DY688059.1|DY688059
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
EST: gi|148971164|gb|EE022018.2|EE022018
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
EST: gi|78113588|gb|DV531979.1|DV531979
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
EST: gi|76014611|gb|DT941781.1|DT941781
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
EST: gi|211049245|gb|FK977495.1|FK977495
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACA
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACA
EST: gi|148932641|gb|EC876549.2|EC876549
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
EST: gi|149059442|gb|EE156927.2|EE156927
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
EST: gi|71329061|gb|DR801238.1|DR801238
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
EST: gi|148942515|gb|EC887530.2|EC887530
EST:     GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAA                         GGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC
genomic: GAAGCAAACGTCAAGAAGATTGTTACTGTAGCACGCGATACGTATGAGAAgtaagtcact ... cttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatattatgctaaaatgtgaacataacattgtgacgattaattcttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTCAAGCTTGATAAGGAAAGTAGCTTCAGATAATGTGTTCGTCATCCAG
                                       ttaattcttcttcc  CT-rich tract
                                      attaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttttataactttctcaaaatcaggaagtcctatattggcttttgaatattatgctaaaatgtgaacataacattgtgacgattaattcttcttccagGGAAGGTCCGACGTTAGTCGTTGCTTGTGGCTGGGACACCATATCATATTCAAGCTTGATAAGGAAAGTAGCTTCAGATAATGTGTTCGTCATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA