Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcgacacacccaactttgcgttgatctctcgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTCATCTTCTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAG

Basic information

species Selaginella moellendorffii
transcript EFJ23827
intron # 2
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|169114942|gb|FE515891.1|FE515891
EST:     TGGTTCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169050296|gb|FE457531.1|FE457531
EST:     TGGTTCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169076892|gb|FE485285.1|FE485285
EST:     TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169097547|gb|FE497989.1|FE497989
EST:     TGGTTCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169024131|gb|FE432496.1|FE432496
EST:     TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGG
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGG
EST: gi|169038977|gb|FE449694.1|FE449694
EST:     TGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169021766|gb|FE430413.1|FE430413
EST:     GGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCANCA-G                         CCCCAAAAGGAGGATGAGATG
genomic: GGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCA-CAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATG
EST: gi|169075809|gb|FE483313.1|FE483313
EST:     TGGTTCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169076893|gb|FE485286.1|FE485286
EST:     GGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCANCA-G                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGG
genomic: GGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCA-CAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGG
EST: gi|169042208|gb|FE454251.1|FE454251
EST:     TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169095398|gb|FE497504.1|FE497504
EST:     TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169029819|gb|FE438387.1|FE438387
EST:     TGGTTCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169026883|gb|FE434234.1|FE434234
EST:     TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
EST: gi|169114943|gb|FE515892.1|FE515892
EST:     TGGTTCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAG                         CCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC
genomic: TGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTC

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), 34 (downstream exon)
Score: 37

CGTGGTGAGCTGCTGCCGGATTGTCATCGCAAACTGCGGGGACTCGCGGGTGGTGCTTTGCCGCGGTGGTCGGGCCATTCCACTCTCGGTGGATCACAAGgtacgttcga ... cgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTCATCTTCTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgttcgacacacccaactttgcgttgatctctcgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTCATCTTCTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAG
                                  cgttgat  putative branch site (score: 37)
                                        tctctcgt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttcgacacacccaactttgcgttgatctctcgtgttccagCCCGAAAAGGAGGATGAGATGCAACGCATCGAGGACGCCGGCGGTCGAGTCATCTTCTGGAACGGCTACCGAGTCATGGGAATGCTGGCCATGTCCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG