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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacgaagactttttttttttcttatttcatttaatcgtattctccgtttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT

Basic information

species Selaginella moellendorffii
transcript EFJ09546
intron # 5
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|169115410|gb|FE516151.1|FE516151
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169029569|gb|FE438930.1|FE438930
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|70669547|gb|DN838124.1|DN838124
EST:     GCTGCGAGTTGCTCTCGGTGTTGTGGACGCAGAGTATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169079267|gb|FE490156.1|FE490156
EST:     GCTGCGAGTTGCTCTCGGTGTTGTGGACGCAGAGTATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169075081|gb|FE481454.1|FE481454
EST:     GCTGCGAGTTGCTCTCGGTGTTGTGGACGCAGAGTATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169088397|gb|FE495443.1|FE495443
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169078772|gb|FE489622.1|FE489622
EST:     GCTGCGAGTTGCTCTCGGTGTTGTGGACGCAGAGTATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169041742|gb|FE449300.1|FE449300
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169106155|gb|FE507947.1|FE507947
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169099588|gb|FE502621.1|FE502621
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169054031|gb|FE461330.1|FE461330
EST:     GCTGCGAGTTGCTCTCGGTGTTGTGGACGCAGAGTATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169088169|gb|FE493395.1|FE493395
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|70670735|gb|DN839312.1|DN839312
EST:     GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169045092|gb|FE450936.1|FE450936
EST:     GCTGCGAGTTGCTCTCGGTGTTGTGGACGCAGAGTATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
EST: gi|169078721|gb|FE487556.1|FE487556
EST:     GCTGCGAGTTGCTCTCGGTGTTGTGGACGCAGAGTATGGCATGGGAACTG                         CCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG
genomic: GCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGG

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: 68

GTGGGAGATTTGAAAGGAATACTTGGGATTTTCTTAGCGAATGTTTTTCGGCTGCGAGTTGCTCTCGGTGTCGTGGACGCAGAATATGGCATGGGAACTGgtaaaacgaa ... ttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaagactttttttttttcttatttcatttaatcgtattctccgtttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT
                          atttaat  putative branch site (score: 68)
                                   tattctccgtttcttt  putative PPT
     actttttttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacgaagactttttttttttcttatttcatttaatcgtattctccgtttctttgcagCCAATACAGCCATGGTGTATCACAACAAGAAACTTTTAGCACTATTAGAGGCTGACAAACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA