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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacatataaactatttaacacctaatattcagtaatcagtaatttattatatggaggctacaaattgttgagctgtttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACAAATCTGCTAATGTAACAGCCTGTAGG

Basic information

species Zea mays
transcript GRMZM2G303631_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303631_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 5
gtaagcacatataaactatttaacacctaatattcagtaatcagtaatttattatatggaggctacaaattgttgagctgtttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACAAATCTGCTAATGTAACAGCCTGTAGG
           |||   | | |||  | | | |  | || || ||| ||  ||  ||  || || |  | | ||||| ||||| || ||||| || || || |||||||| ||||||||||||||||| ||||||||||||||| |||||||||||||||| || |||
----------gtaagtcaataaactac-attttcgactattctgtatttagttgaatacagactgctgagtcttgagttgtttcaatacagAAATGGAAACTAATGAGTGCCTGAATGACAACGGGGGTTGCTGGCAAGACAAAGCTGCTAATGTAACAGCTTGCAGG
















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|5847202|gb|AW000281.1|AW000281
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|5325106|gb|AI783297.1|AI783297
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|211449604|gb|FL033165.1|FL033165
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|211156293|gb|FL375842.1|FL375842
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|32850609|gb|CD990290.1|CD990290
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|91054221|gb|EB164639.1|EB164639
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|211449603|gb|FL033164.1|FL033164
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|211449602|gb|FL033163.1|FL033163
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|211229612|gb|FL380029.1|FL380029
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA
EST: gi|211212797|gb|FL419176.1|FL419176
EST:     TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATG                         ATATAGAGACAAATGAGTGTCTGAWTGACAACGGGGGCTGCTGGCAAGACA
genomic: TTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacat ... ttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcagtaatttattatatggaggctacaaattgttgagctgtttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACAAATCTGCTAATGTAACAGCCTGTAGG
      agtaatttattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacatataaactatttaacacctaatattcagtaatcagtaatttattatatggaggctacaaattgttgagctgtttgaaaacagATATAGAGACAAATGAGTGTCTGAATGACAACGGGGGCTGCTGGCAAGACAAATCTGCTAATGTAACAGCCTGTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA