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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatctagctaaggagttatatctttcttccttttggatttgtacttgctaaatattagttaatctagatggctcgtgtatgatatttccccctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG

Basic information

species Zea mays
transcript GRMZM5G840909_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 1
aatctagctaaggagttatatctttcttccttttggatttgtacttgct-aaatattagttaatctagatggctcgtgtatgatatttccccctcttg-tagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG
  || |||  |  | |  |   | |  ||  ||    || | |   ||| ||| | |  ||   | ||  | |   || || || ||   |  | ||   ||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||
-ctccagcctaaaattctttaatataatcacttcttgttgggaggagctgaaacaatcattt-ccaagcagtcaaatgaattattttcttcatttttaacagTTGTGGAATCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG
















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|74244654|gb|DT652568.1|DT652568
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
EST: gi|211533256|gb|FL397681.1|FL397681
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
EST: gi|211111076|gb|FL388624.1|FL388624
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTC
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
EST: gi|93012688|gb|EB638208.1|EB638208
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
EST: gi|211332537|gb|FL409858.1|FL409858
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGTC
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
EST: gi|211194115|gb|FL380863.1|FL380863
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
EST: gi|89252884|gb|DY624670.1|DY624670
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTC
EST: gi|211162917|gb|FL392799.1|FL392799
EST:     TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGG                         TTGTGGAGTCCAAGGCACGGAACGATCTCAGTTGCTTCAGCATTTGCTGGT
genomic: TGCAATCTCGGCCGTTTCCGCTCCCGCCATCGCCATGGAGGAGGCCAAGGgtaggtctac ... cctcttgtagTTGTGGAGTCCAAGG-ACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctaaatattagttaatctagatggctcgtgtatgatatttccccctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG
                                     tatttccccctcttgt  CT-rich tract
     aatattagttaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatctagctaaggagttatatctttcttccttttggatttgtacttgctaaatattagttaatctagatggctcgtgtatgatatttccccctcttgtagTTGTGGAGTCCAAGGACGGGACGATCTCAGTTGCTTCAGCATTTGCTGGTCATCAGGAAG

- - - - - - - - - - - - - - - - - - - - -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtatg