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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctcttgcatgatcattaacagaagcaaaaatcatccttttgtttctttatgtttcccaataaagaaaaaaggggaaagtttctggtgtagtgtg...

Basic information

species Zea mays
transcript GRMZM2G099980_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099980_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g01170.1 (Oryza sativa), 5'ss of exon 4
ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctcttgcatgatcattaacagaagcaaaaatcatccttttgtttctttatgtttcccaat--aaagaa----aaaaggggaaagtttctggtgtagtgtg
| | || || || ||||||||||| ||||||||||||||||||||||||||||||||||| |||||| |||||||||| ||||| ||||| |||||||||||    |||||||    |||    |  | ||| | |  ||     ||| | |  |  | |  |  |  |  |||     |   |   ||  | |  |||| |    
ATTAAAGGATTTTTCTAACAAAAGCGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCCATGCTTCTAGATGTTCTTGAAGGATATCTCAAATATGAGgta---ctcttgctaactcagagtctcaggcagacagtatataaatgtatatggaaatctttctgtttatggaattttgatttgattaaaatccctgtgttgc---

upper sequence: GRMZM2G099980_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 4
ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctcttgcatgatcattaacagaagcaaaaatcatccttttgtttctttatgtttcccaat--aaagaa----aaaaggggaaagtttctggtgtagtgtg
| | || || || ||||||||||| |||||||||||||||||||||||||||||||| || |||||| |||||||||| ||||| ||||| |||||||||||    |||||||    |||    |  | ||| | |  ||     ||| | |  |  | |  |  |  |  |||     |   |   ||  | |  |||| |    
ATTAAAGGATTTTTCTAACAAAAGCGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGCCCCATGCTTCTAGATGTTCTTGAAGGATATCTCAAATATGAGgta---ctcttgctaactcagagtctcaggcagacagtatataaatgtatatggaaatctttctgtttatggaattttgatttgattaaaatccctgtgttgc---
















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|60349637|gb|DN216610.1|DN216610
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|32910582|gb|CF015394.1|CF015394
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|31612036|gb|CD568658.1|CD568658
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|5895715|gb|AW036961.1|AW036961
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|20507094|gb|BQ279481.1|BQ279481
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|5006225|gb|AI712287.1|AI712287
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|71428991|gb|DR810041.1|DR810041
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|33770989|gb|CF273283.1|CF273283
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|60349938|gb|DN216911.1|DN216911
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|67033833|gb|CO462582.1|CO462582
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|71428990|gb|DR810040.1|DR810040
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|76283944|gb|DV023512.1|DV023512
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211426560|gb|FL408424.1|FL408424
EST:     AGAGTGGTCCAATGCTTTTAGATGTTCTCGAAAGTTATCTGAAATATGAG                         AATTTGTCTCAAACAATGATGGGCGGCAGGANNGATGATGAGTGCAGAATC
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAG-GATGATGAGTTCAGAATC
EST: gi|20513022|gb|BQ280208.1|BQ280208
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|26457465|gb|CA829048.1|CA829048
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|71427898|gb|DR808948.1|DR808948
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|71449093|gb|DR830143.1|DR830143
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|78025444|gb|DV493831.1|DV493831
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|78544427|gb|DV621925.1|DV621925
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|32944273|gb|CF049092.1|CF049092
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|60359114|gb|DN226087.1|DN226087
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|91048017|gb|EB158435.1|EB158435
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGGAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|21626078|gb|BQ620999.1|BQ620999
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211383597|gb|FL452880.1|FL452880
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGSCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211054006|gb|FL385558.1|FL385558
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCA
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCA
EST: gi|61118250|gb|DN559211.1|DN559211
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|31612035|gb|CD568657.1|CD568657
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|12970923|gb|BG267226.1|BG267226
EST:     AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT

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: 253

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 117

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTAT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 144

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCAATGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAACAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGTTGAACATCGGAGCATGAGGAGGGCACCATTAT