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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcctatcttttttatatcgtctttaatgcttattctaaatgatgtatagAGTGAATCATCTCCCAAGTCATTGAAAGAAGGTTCTGAGCCTCCTACATTTTGGAATGCTCTTGGAGGAAAGAAGGTATATCCCAGCCAGAGAGAACTTG

Basic information

species Selaginella moellendorffii
transcript EFJ19773
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|169080133|gb|FE487941.1|FE487941
EST:     GTACCCTTGAGGAACAACAAGTTGCCGCACGAATTGCTACGTCATTGAAG                         AGTGAATCATCTCCCAAGTCATTGAAAGAAGGTTCTGAGCCTCCTACATTT
genomic: GTACCCTTGAGGAACAACAAGTTGCCGCACGAATTGCTACGTCATTGAAGgtaactccta ... tgatgtatagAGTGAATCATCTCCCAAGTCATTGAAAGAAGGTTCTGAGCCTCCTACATTT
EST: gi|169073702|gb|FE481388.1|FE481388
EST:     GTACCCTTGAGGAACAACAAGTTGCCGCACGAATTGCTACGTCATTGAAG                         AGTGAATCATCTCCCAAGTCACTGAAAGAAGGTTCTGAGCCTCCTACATTT
genomic: GTACCCTTGAGGAACAACAAGTTGCCGCACGAATTGCTACGTCATTGAAGgtaactccta ... tgatgtatagAGTGAATCATCTCCCAAGTCATTGAAAGAAGGTTCTGAGCCTCCTACATTT

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), 35 (downstream exon)
Score: 14

CTTCATTTTTCAGTCTGCTAAGACTTATTTGCTATGGTTTGGAAGTTTCAGTACCCTTGAGGAACAACAAGTTGCCGCACGAATTGCTACGTCATTGAAGgtaactccta ... tgatgtatagAGTGAATCATCTCCCAAGTCATTGAAAGAAGGTTCTGAGCCTCCTACATTTTGGAATGCTCTTGGAGGAAAGAAGGTATATCCCAGCCAGAGAGAACTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaactcctatcttttttatatcgtctttaatgcttattctaaatgatgtatagAGTGAATCATCTCCCAAGTCATTGAAAGAAGGTTCTGAGCCTCCTACATTTTGGAATGCTCTTGGAGGAAAGAAGGTATATCCCAGCCAGAGAGAACTTG
                                      ttctaaa  putative branch site (score: 14)
          tatcttttttatat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcctatcttttttatatcgtctttaatgcttattctaaatgatgtatagAGTGAATCATCTCCCAAGTCATTGAAAGAAGGTTCTGAGCCTCCTACATTTTGGAATGCTCTTGGAGGAAAGAAGGTATATCCCAGCCAGAGAGAACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG