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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcccgcattgctcttttattttttttctaatgcatacctcttcatagaatgtatcatcaactctaaaccaaatctggctgggtgtaacatttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGCATCACTGTCGTACTGAAGAACGCGATAATTGCTGATGGATTGGTCATAT

Basic information

species Zea mays
transcript GRMZM2G391936_T05
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 14
----------tctgcccgcattgctcttttattttttttctaatgcatacctcttcatagaatgtatcatcaactctaaaccaaatctggctgggtgtaacatttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGCATCACTGTCGTACTGAAGAACGCGATAATTGCTGATGGATTGGTCATAT
           |     |    |||     |  |   ||| ||  |  ||| ||||  |  || |   ||      |        ||||  ||||| | | ||||||  ||||||| | ||||| ||||| || || |||||||||||||| ||||| ||||||||  ||||| | |||||| |||||||||| |||||||| ||||| |
ggctagctccacaaggtggtgggctagacgacctaggttcgaagcctcaccccttctaattatttgatattgtggttg-------tctg-ttgggtcttaaatttca--gGGTGTACAGGAAGCAGATAGGACCTCTGAAGGCTTCTACATCCGATCAGGCATCACCATCGTATTAAAGAACTCGATAATTGCAGATGGATTAGTCATCT
















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|91874077|gb|EB404034.1|EB404034
EST:     TTGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|18178292|gb|BM379502.1|BM379502
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|71757054|gb|DR954991.1|DR954991
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|13236975|gb|BG354989.1|BG354989
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|71324302|gb|DR798853.1|DR798853
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|27753904|gb|BM378096.1|BM378096
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|71429962|gb|DR811012.1|DR811012
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|24763417|gb|CA398592.1|CA398592
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|211232745|gb|FL322840.1|FL322840
EST:     AGACAAGAATGCGAGGATAGGGAAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATA
genomic: AGACAAGAATGCGAGGATAGGGAA-GAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATA
EST: gi|110195335|gb|EC877232.1|EC877232
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|13558450|gb|BG549806.1|BG549806
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|31363279|gb|CD447636.1|CD447636
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTTTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|13126504|gb|BG317074.1|BG317074
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|211470047|gb|FL442813.1|FL442813
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|38688212|gb|CK145243.1|CK145243
EST:     TAGACCAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|71323466|gb|DR798382.1|DR798382
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|89763297|gb|DY690558.1|DY690558
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|32850355|gb|CD990036.1|CD990036
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGAGGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|16377759|gb|BI992107.1|BI992107
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|31348918|gb|CD433275.1|CD433275
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|12967897|gb|BG264844.1|BG264844
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|50335821|gb|CO530947.1|CO530947
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|31362917|gb|CD447274.1|CD447274
EST:     TACACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|16378153|gb|BI992295.1|BI992295
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
EST: gi|78103575|gb|DV522003.1|DV522003
EST:     TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAA                         GGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC
genomic: TAGACAAGAATGCGAGGATAGGGAAGAAAGTGGTAATCTCCAACTCTGAAgtaagttgat ... catttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagaatgtatcatcaactctaaaccaaatctggctgggtgtaacatttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGCATCACTGTCGTACTGAAGAACGCGATAATTGCTGATGGATTGGTCATAT
                                       gtgtaac  putative branch site (score: 3)
                                          taacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcccgcattgctcttttattttttttctaatgcatacctcttcatagaatgtatcatcaactctaaaccaaatctggctgggtgtaacatttcacagGGTGTAGATGAAGCTGATAGAACTTCCGAAGGCTTCTACATTCGATCTGGCATCACTGTCGTACTGAAGAACGCGATAATTGCTGATGGATTGGTCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA