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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggaaaaggttcttcattttatctcttgcaattgtccctcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTAGCCAAGGAAATTTTCAATCAGACATCAGAGGAGAATGAAGCCTATAATT

Basic information

species Selaginella moellendorffii
transcript EFJ12958
intron # 1
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|169071803|gb|FE477167.1|FE477167
EST:     ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAG                         GCAATAAATCATGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
genomic: ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
EST: gi|169098917|gb|FE502314.1|FE502314
EST:     ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAG                         GCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
genomic: ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
EST: gi|169116347|gb|FE517710.1|FE517710
EST:     ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAG                         GCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
genomic: ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
EST: gi|169109328|gb|FE514091.1|FE514091
EST:     ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAG                         GCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
genomic: ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
EST: gi|169045217|gb|FE451450.1|FE451450
EST:     ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAG                         GCAATAAATCATGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
genomic: ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
EST: gi|169101022|gb|FE500935.1|FE500935
EST:     ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAG                         GCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
genomic: ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
EST: gi|169106553|gb|FE503886.1|FE503886
EST:     ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAG                         GCAATAAATCATGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA
genomic: ATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTA

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), 33 (downstream exon)
Score: 11

TCTTGATGATTCTCAAGTTCCAATAATTGATTTCTCTGGTGATCCCAAGTATATAGTAGATGCTATAGCTTGGGCTTGCCAAGAATGGGGTTTTTTCCAGgtagggaaaa ... tcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTAGCCAAGGAAATTTTCAATCAGACATCAGAGGAGAATGAAGCCTATAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagggaaaaggttcttcattttatctcttgcaattgtccctcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTAGCCAAGGAAATTTTCAATCAGACATCAGAGGAGAATGAAGCCTATAATT
                                         ttgtccctcctgtct  CT-rich tract
                   ttcattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggaaaaggttcttcattttatctcttgcaattgtccctcctgtctagGCAATAAATCACGGTGTTCCAATTGCTAGTATGAAAAATGTCCTCAAACTAGCCAAGGAAATTTTCAATCAGACATCAGAGGAGAATGAAGCCTATAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC