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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgataattgttaatatcttgctataaaaaattcggtgtgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCGTACATGGGATTTCCCGGGACAACGGGTGCGCAGTATATTGATTATTTGG

Basic information

species Selaginella moellendorffii
transcript EFJ32221
intron # 20
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|169077179|gb|FE485065.1|FE485065
EST:     TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
genomic: TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
EST: gi|169074122|gb|FE481860.1|FE481860
EST:     TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
genomic: TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
EST: gi|169103235|gb|FE506354.1|FE506354
EST:     TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
genomic: TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
EST: gi|169077279|gb|FE485165.1|FE485165
EST:     CAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
genomic: CAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
EST: gi|169050498|gb|FE459605.1|FE459605
EST:     TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
genomic: TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
EST: gi|169053590|gb|FE463333.1|FE463333
EST:     TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAA-TGAGATATTTGCTTTGAAACCGGCCCCCCATTCA-GTTTC
genomic: TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCC-ATTCAAGTTTC
EST: gi|169039008|gb|FE448256.1|FE448256
EST:     TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
genomic: TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
EST: gi|169032089|gb|FE437994.1|FE437994
EST:     TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAG                         GGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG
genomic: TCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCG

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: 19

GCATTTTAAAGATATGTCGGCGATGTCATCAGACATGATCGCAAGAACGATCGCTGATGATCAAATACAAGTTCTAGTTAATCTGAACGGCTACACGAAGgtcggtgata ... tgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCGTACATGGGATTTCCCGGGACAACGGGTGCGCAGTATATTGATTATTTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcggtgataattgttaatatcttgctataaaaaattcggtgtgtttctcagGGAGCTAAAAATGAGATATTTGCTTTGAAACCGGCCCCCATTCAAGTTTCGTACATGGGATTTCCCGGGACAACGGGTGCGCAGTATATTGATTATTTGG
               tgttaat  putative branch site (score: 19)
                                             tgtttctc  putative PPT
          ataattgttaatatct  TA-rich tract