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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttaggatccctaactggatctgaaaaggatatgtctcaaacatttttatatccacatcatgataaccatgccgtgttcttttttttttaacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGACACGCACTCTCCAGATTCGGATGA

Basic information

species Zea mays
transcript GRMZM2G163159_T05
intron # 4
splice site 3'
intron type U2

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|148937964|gb|EC882197.2|EC882197
EST:     TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACG                         AGATT-GGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGGGAGGA
genomic: TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACGgttagaactt ... taacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
EST: gi|71760032|gb|DR957969.1|DR957969
EST:     TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACG                         AGATT-GGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
genomic: TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACGgttagaactt ... taacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
EST: gi|86473704|gb|DY240074.1|DY240074
EST:     CTTCAGAGAAGACATGGATCTACAAACG                         AGATT-GGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
genomic: CTTCAGAGAAGACATGGATCTACAAACGgttagaactt ... taacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
EST: gi|78093036|gb|DV521410.1|DV521410
EST:     TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACG                         AGATT-GGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
genomic: TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACGgttagaactt ... taacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
EST: gi|78108412|gb|DV526830.1|DV526830
EST:     TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACG                         AGATT-GGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
genomic: TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACGgttagaactt ... taacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
EST: gi|110214716|gb|EC896613.1|EC896613
EST:     TCTTTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACG                         AGATT-GGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
genomic: TCTCTCAGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACGgttagaactt ... taacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
EST: gi|84970115|gb|DV171511.2|DV171511
EST:     AGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACG                         AGATT-GGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA
genomic: AGTTAACCAGAGGATGCTTCAGAGAAGACATGGATCTACAAACGgttagaactt ... taacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatatccacatcatgataaccatgccgtgttcttttttttttaacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGACACGCACTCTCCAGATTCGGATGA
                                          ttttaac  putative branch site (score: 2)
                            ccgtgttctttttttt  CT-rich tract
                                 ttcttttttttttaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttaggatccctaactggatctgaaaaggatatgtctcaaacatttttatatccacatcatgataaccatgccgtgttcttttttttttaacatgtagAGATTGGGCTGTACTGGACTCACTTTCTGAAGCATTTAGGAACTGCGAGGACACGCACTCTCCAGATTCGGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC