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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtgaaaaaacataagtacttccgtatcgacactctaaagtacttacaagtctctttccggatcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAACGATGAGACAGCGCTCTTGAAAGCCGTGGCTCATCAGCCCGTGAGCGTAG

Basic information

species Selaginella moellendorffii
transcript EFJ36576
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|169071628|gb|FE476563.1|FE476563
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169069378|gb|FE479474.1|FE479474
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169068391|gb|FE478981.1|FE478981
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|70670447|gb|DN839024.1|DN839024
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169107395|gb|FE504169.1|FE504169
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169111577|gb|FE511867.1|FE511867
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169020788|gb|FE430189.1|FE430189
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169071994|gb|FE477683.1|FE477683
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169109484|gb|FE514130.1|FE514130
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACCAGGATGTCCCACTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169040444|gb|FE448444.1|FE448444
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|70670124|gb|DN838701.1|DN838701
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169111834|gb|FE511214.1|FE511214
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC
EST: gi|169058162|gb|FE466592.1|FE466592
EST:     AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAG                         ATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTCCCAGTGAAC
genomic: AGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAAC

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: 78

CATGGACTACGCGTTTGGGTTTGTGATCAAGAACGGTGGGCTGGACACCGAGGCCGATTATCCTTACAAGGGCTATGGCACCCGCTGCGACAGGAGCAAGgcaagtgaaa ... atcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAACGATGAGACAGCGCTCTTGAAAGCCGTGGCTCATCAGCCCGTGAGCGTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttccgtatcgacactctaaagtacttacaagtctctttccggatcccaccagATGAACGCCAAAGTTGTGACGATTGATGGCTACGAGGATGTTCCAGTGAACGATGAGACAGCGCTCTTGAAAGCCGTGGCTCATCAGCCCGTGAGCGTAG
                        tacttac  putative branch site (score: 78)
                                              tcccacc  putative PPT
                   taaagta  TA-rich tract