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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accccccaaaaatgtcatgtgtactttggaaaaatgagagtttatgatttttctggcaaattttcttggatgtgcaaatgatggtttcgtttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG

Basic information

species Zea mays
transcript GRMZM2G158261_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158261_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g17920.2 (Oryza sativa), 3'ss of exon 3
accccccaaaaatgtcatgtgtactttggaaaaatgagagtttatgatttttctggcaaat--tttcttggatgtg--caaatgatg--gtttcg----tttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG--
         || |  ||||| ||    | |||   || |||||  || | ||  |  | ||  ||||     |  |  || | | ||  | || |    |||||||||||||||| || ||||||||||||| ||||||||||||||||| |||   
-------ttaattaacatgtatag---gcaaatgagaaagttttggactattaggctagatattttcccaactacgaccagaggctgaagctttgcttttttgtttgcagATAACAGTAGATGGTGAAGTTGCCACTGATCCAGATATGATTCTCAG
















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|211188055|gb|FK976790.1|FK976790
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|33942227|gb|CF348827.1|CF348827
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT-G
EST: gi|211188058|gb|FK976793.1|FK976793
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185662|gb|FK976786.1|FK976786
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185663|gb|FK976787.1|FK976787
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|50333301|gb|CO528427.1|CO528427
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT-G
EST: gi|211185661|gb|FK976785.1|FK976785
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|5268759|gb|AI770723.1|AI770723
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT-G
EST: gi|211185658|gb|FK976782.1|FK976782
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185656|gb|FK976780.1|FK976780
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185660|gb|FK976784.1|FK976784
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT-G
EST: gi|211185657|gb|FK976781.1|FK976781
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211183259|gb|FK976773.1|FK976773
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211188059|gb|FK976794.1|FK976794
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185650|gb|FK976774.1|FK976774
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185652|gb|FK976776.1|FK976776
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185651|gb|FK976775.1|FK976775
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211185654|gb|FK976778.1|FK976778
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|76293168|gb|DV032736.1|DV032736
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT-G
EST: gi|76017214|gb|DT944384.1|DT944384
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT-G
EST: gi|211188057|gb|FK976792.1|FK976792
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|32909407|gb|CF014219.1|CF014219
EST:     GTGGATCAAGAGGATTCATAACGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT--G
EST: gi|58029903|gb|CX725330.1|CX725330
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTGG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCT-G
EST: gi|211185655|gb|FK976779.1|FK976779
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211188054|gb|FK976789.1|FK976789
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
EST: gi|211188056|gb|FK976791.1|FK976791
EST:     GTGGATCAAGAGGATTCGTAATGGGCAG                         ATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
genomic: GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 28 (upstream exon), 47 (downstream exon)
Score: 276

GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG


Block sizes: 28 (upstream exon), 47 (downstream exon)
Score: 105

GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG


Block sizes: 28 (upstream exon), 47 (downstream exon)
Score: 131

GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 123

GTGGATCAAGAGGATTCGTAATGGGCAGgtagggaaaa ... ttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttttctggcaaattttcttggatgtgcaaatgatggtttcgtttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG
                                       tttcgttt  CT-rich tract
            aaattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accccccaaaaatgtcatgtgtactttggaaaaatgagagtttatgatttttctggcaaattttcttggatgtgcaaatgatggtttcgtttgtttgcagATAACCGTTGATGGTGAAGTTGTCACTGATCCAGATATGACTCTG

-cccccca
- - - - - - - -catgtgt
- - - - - - - - - - - - - - gaaaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgatg