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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgcgtctctggattggggcgagggtgatttgattcactggtggtgtgatttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG

Basic information

species Selaginella moellendorffii
transcript EFJ31557
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|169076897|gb|FE485290.1|FE485290
EST:     GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAG                         CTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
genomic: GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAGgtatgcgcgt ... tttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
EST: gi|169029571|gb|FE438932.1|FE438932
EST:     GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAG                         CTGGAGAGCTTACCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
genomic: GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAGgtatgcgcgt ... tttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
EST: gi|169076232|gb|FE485262.1|FE485262
EST:     GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAG                         CTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
genomic: GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAGgtatgcgcgt ... tttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
EST: gi|169028583|gb|FE440440.1|FE440440
EST:     GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAG                         CTGGAGAGCTTACCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
genomic: GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAGgtatgcgcgt ... tttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
EST: gi|169024266|gb|FE433060.1|FE433060
EST:     GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAG                         CTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
genomic: GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAGgtatgcgcgt ... tttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
EST: gi|169020135|gb|FE428522.1|FE428522
EST:     GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAG                         CTGGAGAGCTTACCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC
genomic: GCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAGgtatgcgcgt ... tttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAAC

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), 33 (downstream exon)
Score: 36

GATCCGCAAGAACAAGCGCGACGAGAATCTCATGAAGAAGCGGCGAGAGGGCATGCAGCCGCAGCACTTTATGACGCCCGGATCGATCGTGGAGAGAAAGgtatgcgcgt ... tttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctctggattggggcgagggtgatttgattcactggtggtgtgatttccttcagCTGGAGAGCTTGCCCGTGATGGTGAGCGGTGTCTGGTCTGACGATCCCAACTTGCAAGTCGAGGCGACGACCCAGTTCCGGAAGCTACTGTCAATTG
                       atttgat  putative branch site (score: 36)
                                             tttccttc  putative PPT
                       atttgatt  TA-rich tract