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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatgggatttgtcaatggatgtggaatttggttattggtttaaagggttttatgtggcatgatacttatcaatatgctttgtggaactgttgtg...

Basic information

species Zea mays
transcript GRMZM2G009876_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 6
GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatgggatttgtcaatggatgtggaatttggttattggtttaaa---gggttttatgtggcatg-atacttatcaatatgctttgt-ggaactgttgtg
||||| ||||| |||||||||||||||||||| ||| |||||||||||||| ||||||||||||||    |  || |||| | |||  |  |    |||| ||| | |   || || ||||     || || | | |   | | |||  | | | ||      
GTCAGACCTGTGGCTGAAGAAGAAATGTTCAAAGTTTTACGAACTGGCAAGAGAAAAAgtaagtgaacctaggtgccaatag-tgtaaatctgtaatattagttgacatttggcttgtatgctcggtgcattcatgtatttgtacttcctcgtagctag----
















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|211143002|gb|FL390386.1|FL390386
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|24764520|gb|CA399684.1|CA399684
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|101382315|gb|EB813213.1|EB813213
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|74232800|gb|DT640714.1|DT640714
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|6918424|gb|AW399954.1|AW399954
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGGACTGGCAAGCGAAAAA                         CCAAGCAGNGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|74232799|gb|DT640713.1|DT640713
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|67038385|gb|CO464715.1|CO464715
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTANAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|211358243|gb|FL402304.1|FL402304
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|148953095|gb|EE152575.2|EE152575
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|13515938|gb|BG518214.1|BG518214
EST:     ATGTTCAGGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: ATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|29946116|gb|CB815987.1|CB815987
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|31350057|gb|CD434414.1|CD434414
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|211251420|gb|FL479566.1|FL479566
EST:     GTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAAACTGGCAAGCGAAAAA                         CCAAGCAGTGGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGA
genomic: GTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAA-CTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGG-AAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGA
EST: gi|4621612|gb|AI612445.1|AI612445
EST:     AAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: AAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|60399997|gb|DN232804.1|DN232804
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|76015209|gb|DT942379.1|DT942379
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAACAGTGGAAGAGAATGGTTACTAAAGCCACCTTT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTT
EST: gi|60351247|gb|DN218220.1|DN218220
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|88757436|gb|DY541577.1|DY541577
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|4776075|gb|AI665078.1|AI665078
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCCCCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
EST: gi|149027253|gb|EE046450.2|EE046450
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT
genomic: TGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGAT

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), 45 (downstream exon)
Score: 158

GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAACGGTTCATTCGGCCAACTGGTCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 83

GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAACGGTTCATTCGGCCAACTGGTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 116

GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAACGGTTCATTCGGCCAACTGGTCT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 58

GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatg ... ttgtactcagCCAAGCAGTGGAAGAGAATGGTTACTAAAGCCACCTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAACGGTTCATTCGGCCAACTGGTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAAgtaagtgatgggatttgtcaatggatgtggaatttggttattggtttaaagggttttatgtggcatgatacttatcaatatgctttgtggaactgttgtg

- - - - -  AGCTGA
- - - - - -  CTGAAG
- - - - - - - TGAAGA
- - - - - - - - AAGAAG
- - - - - - - - -  AAGAAA