Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcgtagtctaaatcaaagtttgtcaggaatttgagttgtttcctttggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAAGAAAAGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ34631
intron # 14
splice site 3'
intron type U2

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|169030971|gb|FE440332.1|FE440332
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169024270|gb|FE435222.1|FE435222
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169052463|gb|FE462271.1|FE462271
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169069504|gb|FE480575.1|FE480575
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169115759|gb|FE517345.1|FE517345
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169107240|gb|FE504118.1|FE504118
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169070626|gb|FE480085.1|FE480085
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169082584|gb|FE489068.1|FE489068
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169081354|gb|FE489292.1|FE489292
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169076790|gb|FE485833.1|FE485833
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169063160|gb|FE471682.1|FE471682
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169081355|gb|FE489293.1|FE489293
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAANCA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAA-CA
EST: gi|169092697|gb|FE494926.1|FE494926
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169064335|gb|FE471898.1|FE471898
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169044544|gb|FE450609.1|FE450609
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169034852|gb|FE444041.1|FE444041
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
EST: gi|169095446|gb|FE497552.1|FE497552
EST:     TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAA                         AATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA
genomic: TGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAA

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 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 23 (downstream exon)
Score: 14

AATTCTCAAAGTTATACTTAGTGACGAGGATCTTTCCCCCGATTTTAACATGGAGGAAGTGGCAGCGGCGGCAGATGGGTATTCCGGGAGCGATTTGAAAgtgagctcgt ... tggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAAGAAAAGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtagtctaaatcaaagtttgtcaggaatttgagttgtttcctttggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAAGAAAAGAAG
     gtctaaa  putative branch site (score: 14)
                                   ttgtttccttt  putative PPT
        taaatcaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcgtagtctaaatcaaagtttgtcaggaatttgagttgtttcctttggcgtgtagAATCTGTGCACAACGGCGGCCTACATCCGGATACGAGAACTCTTGGAACAAGAAAAGAAG

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