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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctcttgcgtgatcattaacagaagcaaaaatcatccttttgtttctttatgttttccgaaaaagaaaaaagggggaaagctccttgtgtagtgt...

Basic information

species Zea mays
transcript GRMZM2G151268_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151268_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g01170.1 (Oryza sativa), 5'ss of exon 4
ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctcttgcgtgatcattaacagaagcaaaaatcatccttttgtttctttatgt-tttccgaaaaagaaa----aaagggggaaagctccttgtgtagtgt
| | || || || ||||||||||| |||||||||||||||||||||||||||||||||||  ||||| |||||||||| ||||| ||||| |||||||||||    |||||||    |||    |  | ||| | |  ||     ||| | |  |  | |||| |   | | ||     |   |   ||  ||| ||||| |   
ATTAAAGGATTTTTCTAACAAAAGCGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCCATGCTTCTAGATGTTCTTGAAGGATATCTCAAATATGAGgta---ctcttgctaactcagagtctcaggcagacagtatataaatgtatatggaaatctttctgtttatggaattttgatttgattaaaatccctgtgttgc--

upper sequence: GRMZM2G151268_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 4
ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctcttgcgtgatcattaacagaagcaaaaatcatccttttgtttctttatgt-tttccgaaaaagaaa----aaagggggaaagctccttgtgtagtgt
| | || || || ||||||||||| |||||||||||||||||||||||||||||||| ||  ||||| |||||||||| ||||| ||||| |||||||||||    |||||||    |||    |  | ||| | |  ||     ||| | |  |  | |||| |   | | ||     |   |   ||  ||| ||||| |   
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|45847355|gb|CN071298.1|CN071298
EST:     TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGCCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|21432449|gb|BQ547939.1|BQ547939
EST:     AAAGTGGTCCCCTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|23357627|gb|BU645276.1|BU645276
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|60359679|gb|DN226652.1|DN226652
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|78122445|gb|DV540829.1|DV540829
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|89106102|gb|DY576319.1|DY576319
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|26557650|gb|CA829885.1|CA829885
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATTTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211144130|gb|FL475584.1|FL475584
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAACCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|21809549|gb|BQ667867.1|BQ667867
EST:     TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: TGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211194039|gb|FL029192.1|FL029192
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|60348471|gb|DN215444.1|DN215444
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|29945211|gb|CB815526.1|CB815526
EST:     AAAGTGGTCCNCTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
EST: gi|211191650|gb|FL029191.1|FL029191
EST:     AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAG                         AATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT
genomic: AAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCT

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), 47 (downstream exon)
Score: 137

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctct ... ttttggtcagAATTTGTCTCAAGCAAGGATGGGCGGCAGGAGGATGATGAGTTCAGAATCTGATCCATCACTAAATGCTGAACATCGGAGCATGAGGAGGGCACCATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGAAAGACTTCTCTAACAAAAGTGGAGCTGAAGGGAGCAGGAGTGCTGAAAGTGGTCCACTGCTTTTAGATGTTCTCGAAGGTTATCTGAAATATGAGgtttatctcttgcgtgatcattaacagaagcaaaaatcatccttttgtttctttatgttttccgaaaaagaaaaaagggggaaagctccttgtgtagtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaaa