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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcattgttatgctgcagcttcttcgcagttatttgtggcataaaaagagatctaactgggacactattttatttttcctttgaaag

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g10310.2 (Oryza sativa), 5'ss of exon 9
GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcattgttatgctgcagcttcttcgcagttatttgtggcataaaaagagatctaactgggacactattttatttttcctttgaaag---------------
||||| |||||||| || ||| ||||||||||||| ||| ||||||| || ||||||||||| ||| |   || | |||  |||  ||||||     ||||| |   || || ||| || | | |   |||  |  | ||  ||  |     |                
GAACCTGAACCTTTGCCTTACTTAGCTGAAAAGAACCACGTAAACTACGATATTCCTCTTGAGgtaggattttctcatg--gca-tttcttcttttatattttta-tattaatagatatttgattaaaacataaactgatgattattactgcatttcattttctgtaag
















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|60358486|gb|DN225459.1|DN225459
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|32937713|gb|CF042532.1|CF042532
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|60351022|gb|DN217995.1|DN217995
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|60401451|gb|DN234258.1|DN234258
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|16918483|gb|BM073768.1|BM073768
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|60338752|gb|DN205725.1|DN205725
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|60358733|gb|DN225706.1|DN225706
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|19058676|gb|BM737343.1|BM737343
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTGGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGNCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|211167201|gb|FL456897.1|FL456897
EST:     CATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCYTAAAGWTCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: CATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|22490645|gb|BU050568.1|BU050568
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|24769868|gb|CA404997.1|CA404997
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|211126137|gb|FL125779.1|FL125779
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|94474487|gb|EB703445.1|EB703445
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|87154062|gb|DY398851.1|DY398851
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|71424524|gb|DR806343.1|DR806343
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|5686716|gb|AI939809.1|AI939809
EST:     ATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: ATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|60397238|gb|DN230054.1|DN230054
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|5740098|gb|AI947788.1|AI947788
EST:     ATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: ATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|149106512|gb|EE188404.2|EE188404
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
EST: gi|86466217|gb|DY232590.1|DY232590
EST:     TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAA                         GTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT
genomic: TACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACT

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: 128

GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 129

GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 137

GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcatt ... cctttgaaagGTCTTGATTAAGCCTAAAGATCAAAATGTTGCACTAATTGTCACAAAAACTAATTTCAAGCATCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCCGAACCTTTACCATACCTAGCTGAAAAGAATCACATAAACTATGACATTCCTCTTGAAgtatggcattgttatgctgcagcttcttcgcagttatttgtggcataaaaagagatctaactgggacactattttatttttcctttgaaag

- - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - -  AAAGAA