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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttttgctcatagcatgtgtctgtaaagcatgtatgtgttctaaataatatgtggtgcattatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGCCTGGTTATGATAGCGAAACAGCAAGGCTGGCGACAACTTTTCTCAGGAT

Basic information

species Zea mays
transcript GRMZM2G161299_T01
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|67010867|gb|CO439616.1|CO439616
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|16926745|gb|BM079813.1|BM079813
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|71761231|gb|DR959168.1|DR959168
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|76294059|gb|DV033627.1|DV033627
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|71435374|gb|DR816424.1|DR816424
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|94477872|gb|EB706830.1|EB706830
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|71757614|gb|DR955551.1|DR955551
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|71442969|gb|DR824019.1|DR824019
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
EST: gi|71760931|gb|DR958868.1|DR958868
EST:     TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAG                         GTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC
genomic: TAGGTCAGACAATAACATACCCCCTAGATGTTGTTAGGCGACAAATGCAGgtattgtttt ... ttatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtctgtaaagcatgtatgtgttctaaataatatgtggtgcattatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGCCTGGTTATGATAGCGAAACAGCAAGGCTGGCGACAACTTTTCTCAGGAT
                        ttctaaa  putative branch site (score: 2)
                      tgttctaaataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttttgctcatagcatgtgtctgtaaagcatgtatgtgttctaaataatatgtggtgcattatttacagGTTCAAGCCCTTTCGTCATCCAGCCTTGTGGGTAGGGGAACATTTGAAAGCCTGGTTATGATAGCGAAACAGCAAGGCTGGCGACAACTTTTCTCAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG