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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatgcttttcttcacatttttctaaaaaaactaagagccttcagtgagtctaactctctaatttgtctttgcgtttctgttgaatcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG

Basic information

species Zea mays
transcript GRMZM2G069174_T02
intron # 5
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|94479305|gb|EB708263.1|EB708263
EST:     AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGGCAGTGCAGTT
genomic: AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
EST: gi|93282822|gb|EB675086.1|EB675086
EST:     AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
genomic: AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
EST: gi|74246261|gb|DT654175.1|DT654175
EST:     AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
genomic: AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
EST: gi|76015058|gb|DT942228.1|DT942228
EST:     AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
genomic: AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
EST: gi|37425821|gb|CF650659.1|CF650659
EST:     CATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGACTTTGAGGATGCCAGTGCAGTT
genomic: CATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
EST: gi|101391401|gb|EB817635.1|EB817635
EST:     AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
genomic: AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
EST: gi|32838442|gb|CD978120.1|CD978120
EST:     AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
genomic: AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
EST: gi|71763868|gb|DR961805.1|DR961805
EST:     AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAG                         ATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT
genomic: AGAGATTTGGAACCATTAAACATGAAGGCATCCAAGTTAGAAGCAACAAGgtgcatgctt ... atcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagtgagtctaactctctaatttgtctttgcgtttctgttgaatcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG
                  tctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatgcttttcttcacatttttctaaaaaaactaagagccttcagtgagtctaactctctaatttgtctttgcgtttctgttgaatcaacacagATCCAAGGGTTTTGCTATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC