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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccacacacttgttctctctttctgtttccaagctgaatggctttcttttgtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAGAGCGATGAATTTAACTTTGCATCGTCCAGAGTCGAGGGAATTCCAAACA

Basic information

species Selaginella moellendorffii
transcript EFJ07565
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|169020544|gb|FE429802.1|FE429802
EST:     TCTTGAAGCANGGAGAAGTTTTCANAGTAAATGGCTCTCAAGGATCGCAG                         CTCGATATCGAGGTGACTTTTTCAA-TCCCAAAGGCT
genomic: TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTC-CAAATCCCAAAGGCT
EST: gi|169114759|gb|FE516020.1|FE516020
EST:     TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAG                         CTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
genomic: TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
EST: gi|169028108|gb|FE435960.1|FE435960
EST:     TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAG                         CTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
genomic: TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
EST: gi|169067554|gb|FE475790.1|FE475790
EST:     TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAG                         CTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
genomic: TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
EST: gi|169114760|gb|FE516021.1|FE516021
EST:     TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAG                         CTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
genomic: TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
EST: gi|169037851|gb|FE445760.1|FE445760
EST:     TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAG                         CTCGATATCGAGGTGACTTTTCAAATCCCAAAGGCTCACGCCAACGATGAG
genomic: TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
EST: gi|169026531|gb|FE434792.1|FE434792
EST:     TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAG                         CTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG
genomic: TCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAG

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: 32

GCCAGAGATCAATTCTCTAAGAAAGCATCCAATTCGTCATACAGATTTGCTCTTGAAGCAGGGAGAAGTTTTCAAAGTAAATGGCTCTCAAGGATCGCAGgtaccacaca ... gtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAGAGCGATGAATTTAACTTTGCATCGTCCAGAGTCGAGGGAATTCCAAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacttgttctctctttctgtttccaagctgaatggctttcttttgtccttgcagCTCGATATCGAGGTGACTTTCCAAATCCCAAAGGCTCACGCCAACGATGAGAGCGATGAATTTAACTTTGCATCGTCCAGAGTCGAGGGAATTCCAAACA
                                    ctttcttttgtccttg  CT-rich tract
                                     tttctttt  TA-rich tract