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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttttcttttggtttgatggaactatttgtttttctttgtctaactttgtagagttttcagCGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGCCACAGATCATTATGCCCAGCTGACAGTCACAAGCAAAGAAAAAACAGTC

Basic information

species Selaginella moellendorffii
transcript EFJ22660
intron # 4
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|169031503|gb|FE438968.1|FE438968
EST:     GTATCTTCCGACAGTTCTGTGACACTGGCTCAAAGTGACACGATCAACGT                         CGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGC
genomic: GTATCTTCCGACAGTTCTGTGACACTGGCTCAAAGTGACACGATCAACGTgtgagttttc ... gagttttcagCGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGC
EST: gi|169079036|gb|FE488586.1|FE488586
EST:     GTATCTTCCGACAGTTCTGTGACACTGGCTCAAAGTGACACGATCAACGT                         CGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGC
genomic: GTATCTTCCGACAGTTCTGTGACACTGGCTCAAAGTGACACGATCAACGTgtgagttttc ... gagttttcagCGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGC
EST: gi|169022261|gb|FE431220.1|FE431220
EST:     GTATCTTCCGACAGTTCTGTGACACTGGCTCAAAGTGACACGATCAACGT                         CGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGC
genomic: GTATCTTCCGACAGTTCTGTGACACTGGCTCAAAGTGACACGATCAACGTgtgagttttc ... gagttttcagCGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGC

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: 57

TTATTTTCTGGTTGAAAGCAGCCACATCCAGCAGTGTCGTTGTCTCCTTTGTATCTTCCGACAGTTCTGTGACACTGGCTCAAAGTGACACGATCAACGTgtgagttttc ... gagttttcagCGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGCCACAGATCATTATGCCCAGCTGACAGTCACAAGCAAAGAAAAAACAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggtttgatggaactatttgtttttctttgtctaactttgtagagttttcagCGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGCCACAGATCATTATGCCCAGCTGACAGTCACAAGCAAAGAAAAAACAGTC
                                gtctaac  putative branch site (score: 57)
                                                ttttc  putative PPT
                 tatttgtttttcttt  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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttttcttttggtttgatggaactatttgtttttctttgtctaactttgtagagttttcagCGATGGCACGAAGGGGTGGACAAAGCAGGAGATCGTCTTGAAAGCACAAGCCACAGATCATTATGCCCAGCTGACAGTCACAAGCAAAGAAAAAACAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA