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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaattctgagctaatctttggaatgcctatatgacatgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCACAAAG

Basic information

species Selaginella moellendorffii
transcript EFJ20638
intron # 25
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|169099051|gb|FE501772.1|FE501772
EST:     GAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCA                         ATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC
genomic: GAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCAgtaagaaaat ... tgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC
EST: gi|169064420|gb|FE472087.1|FE472087
EST:     GAGGCCTTTGTTATGGGGACGTNTGACTCGTGCCAACAACTGTTCTACCA                         ATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC
genomic: GAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCAgtaagaaaat ... tgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC
EST: gi|169099052|gb|FE501773.1|FE501773
EST:     GAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCA                         ATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC
genomic: GAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCAgtaagaaaat ... tgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC
EST: gi|169104104|gb|FE505117.1|FE505117
EST:     GAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCA                         ATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC
genomic: GAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCAgtaagaaaat ... tgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCAC

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: 34 (upstream exon), 35 (downstream exon)
Score: 16

GTGCACAGGAGTCACGTTTTCAAGCTCCGAGAGGCCTTTGTTATGGGGACGTTTGACTCGTGCCAACAACTGTTCTACCAgtaagaaaat ... tgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCACAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagaaaattctgagctaatctttggaatgcctatatgacatgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCACAAAG
                 agctaat  putative branch site (score: 16)
        aagaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaattctgagctaatctttggaatgcctatatgacatgtcgagtagATATATCCAGGGTGTTGCTGACGAGATGGTGCTAAACCACGTCGATCCCACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG