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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAGAAATTGTCAAAGCTGATCTTTCCACCAAGACTCTGACTAGTGCAGCTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctatatttcccttctgctgcttatgtatttgtttcctgaatatcttttgatgatggtgcaaaatgttgcccttcaaagctattaaagatttgttcactggttactagttactcctattttttttggcataataatgaaccacaactgtttccacttgctttccag

Basic information

species Zea mays
transcript GRMZM2G084881_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G084881_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 5'ss of exon 6
TACAGAAATTGTCAAAGCTGATCTTTCCACCAAGACTCTGACTAGTGCAGCTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctatatttcccttctgctgcttatgtatttgtttcctgaatatcttttgatgatggtgcaaaatgttgcccttcaaagctattaaagatttgttcactggttactagttactcctattttttttggcataataatgaaccacaactgtttccacttgctttccag
 || ||||||||||||||||||||| || |||||||| |||||||||||| |||||||| ||||||||||||||| ||| ||||||| ||||||||||| ||||      |           |||   |   ||||||||  |         ||| ||    | | |    |||   || | |  |  |     ||| | | || || |                                                              
CACTGAAATTGTCAAAGCTGATCTTGCCTCCAAGACTTTGACTAGTGCAGTTGGAGCAACCTTTACATATGAGATTTTGATCATTGCAACTGGCTCCTCAgtatgttgtga----------actgtgaa---atttgtttaatatcggctcattgctgtcattactatcacttgttatttaca--tgctctttttttatccgcttgtcag-------------------------------------------------------------
















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|32833050|gb|CD972728.1|CD972728
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32837679|gb|CD977357.1|CD977357
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|18963310|gb|BM660362.1|BM660362
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACTGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|87153386|gb|DY398175.1|DY398175
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACTGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32938597|gb|CF043416.1|CF043416
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GCCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|74236615|gb|DT644529.1|DT644529
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32859100|gb|CD998781.1|CD998781
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32933738|gb|CF038550.1|CF038550
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|33103313|gb|CF063273.1|CF063273
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32837255|gb|CD976933.1|CD976933
EST:     CTGGAGCNAACTNTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32828473|gb|CD968151.1|CD968151
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32828494|gb|CD968172.1|CD968172
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32848333|gb|CD988014.1|CD988014
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32850352|gb|CD990033.1|CD990033
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|33101258|gb|CF061218.1|CF061218
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|33102352|gb|CF062312.1|CF062312
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|211263515|gb|FL023464.1|FL023464
EST:     ATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: ATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32847380|gb|CD987061.1|CD987061
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32829258|gb|CD968936.1|CD968936
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32829160|gb|CD968838.1|CD968838
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|4321049|gb|AI467712.1|AI467712
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32940843|gb|CF045662.1|CF045662
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32838469|gb|CD978147.1|CD978147
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|211263516|gb|FL023465.1|FL023465
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32829042|gb|CD968720.1|CD968720
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|4314900|gb|AI444697.2|AI444697
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32830136|gb|CD969814.1|CD969814
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32828804|gb|CD968482.1|CD968482
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32828858|gb|CD968536.1|CD968536
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32850735|gb|CD990416.1|CD990416
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|33101866|gb|CF061826.1|CF061826
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|67018255|gb|CO447004.1|CO447004
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32846066|gb|CD985747.1|CD985747
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
EST: gi|32830261|gb|CD969939.1|CD969939
EST:     CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCG                         GTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT
genomic: CTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATT

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: 363

TACAGAAATTGTCAAAGCTGATCTTTCCACCAAGACTCTGACTAGTGCAGCTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATTCTATATCTAAGGGAAATTGATGATGCTGACAAGCTGGTTGCAGCTATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1171

TACAGAAATTGTCAAAGCTGATCTTTCCACCAAGACTCTGACTAGTGCAGCTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATTCTATATCTAAGGGAAATTGATGATGCTGACAAGCTGGTTGCAGCTATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 632

TACAGAAATTGTCAAAGCTGATCTTTCCACCAAGACTCTGACTAGTGCAGCTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATTCTATATCTAAGGGAAATTGATGATGCTGACAAGCTGGTTGCAGCTATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1272

TACAGAAATTGTCAAAGCTGATCTTTCCACCAAGACTCTGACTAGTGCAGCTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctat ... tgctttccagGTCATAAAGCTCACCGATTTTGGCACACAAGGAGCTGATTCTAACAACATTCTATATCTAAGGGAAATTGATGATGCTGACAAGCTGGTTGCAGCTATCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAGAAATTGTCAAAGCTGATCTTTCCACCAAGACTCTGACTAGTGCAGCTGGAGCAAACTTTACATATGAGATCTTGCTCATTGCTACTGGCTCCTCGgtatacctatatttcccttctgctgcttatgtatttgtttcctgaatatcttttgatgatggtgcaaaatgttgcccttcaaagctattaaagatttgttcactggttactagttactcctattttttttggcataataatgaaccacaactgtttccacttgctttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC