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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACGTCGCCATGGTTCAGGCAGTGAAACTGAAGGTCAGGAAGGAGGGATATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctatcttgaatttttagttctttttgtcaccatcacttatttgttttcttattactcttttggtattgcag

Basic information

species Zea mays
transcript GRMZM2G089466_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089466_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 5'ss of exon 4
GAAACGTCGCCATGGTTCAGGCAGTGAAACTGAAGGTCAGGAAGGAGGGATATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtct-----atcttgaatttttagttctttttgtcacca-----tcacttatttgttttcttattactcttttggtattgcag---------------
|||||| || ||| ||||||| | |||| ||||||| || || || |||||| | |||||||| |||||||||||||| ||||| |||||||| || || ||| | |       |||    |||||  ||   | |||   ||      ||  |||||  | || || |  | | |||    || |                
GAAACGCCGTCATAGTTCAGGAAATGAAGCTGAAGGCCAAGATGGTGGGATAGTAGCTGCAGGGACTGACAAGGAGCGGTCACTATCTGCTGAGGATGCTgtatgcccccctcctctcactttttttttttcatctgttggcagcaaaccaactatttcatatcgtagttatttattgtgcctgtaccctttgattttgcag
















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|5739655|gb|AI947450.1|AI947450
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|71449705|gb|DR830755.1|DR830755
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTTTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|21809832|gb|BQ668150.1|BQ668150
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|116826405|gb|EC870187.1|EC870187
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|9731008|gb|BE509760.1|BE509760
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|60394307|gb|DN227177.1|DN227177
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|71330751|gb|DR802163.1|DR802163
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTTTTTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|76288626|gb|DV028194.1|DV028194
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|30088378|gb|CB886583.1|CB886583
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|13382318|gb|BG458993.1|BG458993
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|60357534|gb|DN224507.1|DN224507
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|32849413|gb|CD989094.1|CD989094
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCCGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|71330752|gb|DR802164.1|DR802164
EST:     TATTGGCTGCACGAACTGACAAGGAGCGATCACTCTCTGCTGAAAACGCA                         GTTTGCTGCATCTGTCTTGCAAAATAAGCGCACAATGATGAGCTCCG
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCG
EST: gi|5819333|gb|AI987539.1|AI987539
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|149084659|gb|EE174144.2|EE174144
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|24763819|gb|CA398990.1|CA398990
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|5901410|gb|AW042510.1|AW042510
EST:     TATTGGCTGCAGGAACTGNCAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCCCAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|14204262|gb|BG837939.1|BG837939
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
EST: gi|60351925|gb|DN218898.1|DN218898
EST:     TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCA                         GTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA
genomic: TATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 161

GAAACGTCGCCATGGTTCAGGCAGTGAAACTGAAGGTCAGGAAGGAGGGATATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAACTTCCATGTGCACACTGTTTCCACAAGGACTGTGTTGATAAATGGCTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

GAAACGTCGCCATGGTTCAGGCAGTGAAACTGAAGGTCAGGAAGGAGGGATATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAACTTCCATGTGCACACTGTTTCCACAAGGACTGTGTTGATAAATGGCTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 288

GAAACGTCGCCATGGTTCAGGCAGTGAAACTGAAGGTCAGGAAGGAGGGATATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAACTTCCATGTGCACACTGTTTCCACAAGGACTGTGTTGATAAATGGCTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 315

GAAACGTCGCCATGGTTCAGGCAGTGAAACTGAAGGTCAGGAAGGAGGGATATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctat ... ggtattgcagGTTTGCTGCATCTGTCTTGCAAAATATGCGCACAATGATGAGCTCCGTGAACTTCCATGTGCACACTGTTTCCACAAGGACTGTGTTGATAAATGGCTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACGTCGCCATGGTTCAGGCAGTGAAACTGAAGGTCAGGAAGGAGGGATATTGGCTGCAGGAACTGACAAGGAGCGATCACTCTCTGCTGAAGACGCAgtacgtctatcttgaatttttagttctttttgtcaccatcacttatttgttttcttattactcttttggtattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA