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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttcattgtttttctgcttctacgatgcttcattaaaggcttacgtgctttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACTCTAAAGCAGGAGTTCTCTCGCTATGGCAACATCACGTCAGCAAAAGTAA

Basic information

species Selaginella moellendorffii
transcript EFJ38579
intron # 5
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|169087005|gb|FE493069.1|FE493069
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
EST: gi|169036917|gb|FE446035.1|FE446035
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
EST: gi|169047279|gb|FE456528.1|FE456528
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
EST: gi|169024783|gb|FE435475.1|FE435475
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
EST: gi|169020196|gb|FE428245.1|FE428245
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
EST: gi|169079669|gb|FE486333.1|FE486333
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
EST: gi|169045998|gb|FE453115.1|FE453115
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
EST: gi|169093873|gb|FE493461.1|FE493461
EST:     TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAG                         GGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT
genomic: TTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACT

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: 32 (upstream exon), 35 (downstream exon)
Score: 22

AACAATATACGTCGGAAGGGCGCAGAAGAAGGCGGAACGTGAGCAGATACTTCGCCGACAATTCGAAGAGAAACGGATGGAACAGTTCCAGAAGTATCAGgtttttcatt ... ttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACTCTAAAGCAGGAGTTCTCTCGCTATGGCAACATCACGTCAGCAAAAGTAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtttttctgcttctacgatgcttcattaaaggcttacgtgctttgcttttagGGAGCCAATTTATATGTGAAAAACCTCGATGATTCCATAGACGATGAAACTCTAAAGCAGGAGTTCTCTCGCTATGGCAACATCACGTCAGCAAAAGTAA
                                 ggcttac  putative branch site (score: 22)
                                           ctttgctttt  putative PPT
                        ttcattaaa  TA-rich tract