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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttactttcttttcgagaactttccttttatctatcgtaacgctcaacacatctgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGCTGATACAATTGAGAGTTTGCGGGAGTATTTACATAAGCGCGGCCGTGAG

Basic information

species Selaginella moellendorffii
transcript EFJ08380
intron # 17
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|169071799|gb|FE477163.1|FE477163
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         ATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169042900|gb|FE450512.1|FE450512
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         GTACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169076023|gb|FE481005.1|FE481005
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         GTACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169028805|gb|FE438036.1|FE438036
EST:     GAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         GTACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: GAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169062412|gb|FE469471.1|FE469471
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         ATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169097496|gb|FE497938.1|FE497938
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         GTACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169083538|gb|FE491410.1|FE491410
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         GTACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169076626|gb|FE484733.1|FE484733
EST:     -TTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         GTACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169083947|gb|FE493587.1|FE493587
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         GTACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
EST: gi|169070007|gb|FE476476.1|FE476476
EST:     CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCA                         ATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC
genomic: CTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGC

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: 34 (upstream exon), 9 (downstream exon)
Score: 3

GCCAACATTAGCGACGAGCTTCCAAAGGAAGAATGGGATTTAGAAGGTCTAGCATCAAAAGTCAAGCAgtgagttttt ... tgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGCTGATACAATTGAGAGTTTGCGGGAGTATTTACATAAGCGCGGCCGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttcgagaactttccttttatctatcgtaacgctcaacacatctgcactgcagATACTGCTTTCTCCTGGATGACTTATCTGTTGAAGTGCTACTAAAAAATGCTGATACAATTGAGAGTTTGCGGGAGTATTTACATAAGCGCGGCCGTGAG
                          tcgtaac  putative branch site (score: 3)
                 ttttatctat  TA-rich tract