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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtatatgaaatgtaaattgtgaaaagtatgctccttgcagattttgctgggattatttttaattgtaaacaattctctctgtag

Basic information

species Zea mays
transcript AC196426.3_FGT007
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC196426.3_FGT007 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 10
GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtatatgaaatgtaaattgtgaaaagtatgctccttgcagattttgctgggattattt--ttaattgtaaacaattctctctgtag
||  ||||||| || || || |||||||| ||||| || |||||||||||| ||||||||||  |   | ||   | | || ||||   | ||||  || | ||| ||   |  ||| | |   | ||  ||||  | | | | |    
GTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTCAAAGAGCAGgttggcat-cgttaagcattagttatgaatc-tgtgcttgttactgatcttctggaaattgtatgactgataataaattaatttatttag--

upper sequence: AC196426.3_FGT007 (Zea mays), 5'ss of exon 9
lower sequence: AT3G13870.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtatatgaaatgtaa---------attgtgaaaagtatgct------ccttgcagattttgctg------ggattatttttaattgtaaacaat--tctctctgtag-------------------
||| |||| || || || ||||||||||||||||||||||||  ||||||| |||||||  || || |   |   | |         ||| || | |  || |       ||||      |||  ||       |||   || ||  ||  |  |||  | | ||| ||                    
GTTGAAGTAGTTGCTCTCTCGAGTTATGAAGAAAAAGAAGAGCAATTCAAAGAGCAGgtctgtttacaattagctttacattttgccattttggagaagatccagggtcaccttatgtgatttattgctcaatagatggcttgtaggtgatattaatgttttttctataatgttttctgtaaatgaaag
















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|211457038|gb|FK967316.1|FK967316
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211043098|gb|FK967329.1|FK967329
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211454906|gb|FK967300.1|FK967300
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211457037|gb|FK967315.1|FK967315
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211454909|gb|FK967303.1|FK967303
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211454913|gb|FK967307.1|FK967307
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211454904|gb|FK967298.1|FK967298
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211043097|gb|FK967328.1|FK967328
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211457040|gb|FK967318.1|FK967318
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211457033|gb|FK967311.1|FK967311
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211454911|gb|FK967305.1|FK967305
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211457035|gb|FK967313.1|FK967313
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211457034|gb|FK967312.1|FK967312
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
EST: gi|211457046|gb|FK967324.1|FK967324
EST:     TTGTCGCACTGTTGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAG                         GTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT
genomic: TTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTT

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: 226

GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTTGCTGGGGATCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 265

GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTTGCTGGGGATCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTTGCTGGGGATCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtat ... ctctctgtagGTTTCTGATTTAAGAGATAGGTTTCAGCATTCAATTGCCCCTGGTGGACTTGCTGGGGATCGTCGTGGTGTTGTCCCAGCTTCAGGTTTCTCATTTAGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAAGTTGTCGCACTGTCGAGTTATGAAGAAAAAGAAGAGTTATTCAAACAGCAGgttggtgtatatgaaatgtaaattgtgaaaagtatgctccttgcagattttgctgggattatttttaattgtaaacaattctctctgtag

- - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - AAGAAG