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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgcgtgtcttaatcccccgattgctcaaagttcccctcgaaatcttccttctcttccagCGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTTTTTCAGCGAGGCGGCGTCCGCGACGAAGCACGTCCCAAGGGCGGTGATG

Basic information

species Selaginella moellendorffii
transcript EFJ09935
intron # 1
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|169098024|gb|FE496858.1|FE496858
EST:     TTCTGCCTGGAGCACGGCATTCAACCCAATGGAAAGGCGATCGATCGCAA                         CGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT
genomic: TTCTGCCTGGAGCACGGCATTCAACCCAATGGAAAGGCGATCGATCGCAAgtaagcgcgt ... tctcttccagCGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT
EST: gi|169050573|gb|FE459641.1|FE459641
EST:     TTCTGCCTGGAGCACGGCATCCAACCGAATGGAAAGGCGATCGATCGCAA                         CGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT
genomic: TTCTGCCTGGAGCACGGCATTCAACCCAATGGAAAGGCGATCGATCGCAAgtaagcgcgt ... tctcttccagCGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT
EST: gi|169073536|gb|FE482652.1|FE482652
EST:     TTCTGCCTGGAGCACGGCATCCAACCGAATGGAAAGGCGATCGATCGCAA                         CGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT
genomic: TTCTGCCTGGAGCACGGCATTCAACCCAATGGAAAGGCGATCGATCGCAAgtaagcgcgt ... tctcttccagCGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT
EST: gi|169101502|gb|FE501475.1|FE501475
EST:     TTCTGCCTGGAGCACGGCATCCAACCGAATGGAAAGGCGATCGATCGCAA                         CGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT
genomic: TTCTGCCTGGAGCACGGCATTCAACCCAATGGAAAGGCGATCGATCGCAAgtaagcgcgt ... tctcttccagCGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTT

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: 29 (upstream exon), 35 (downstream exon)
Score: 10

TACACGTCGGGCAGGCAGGAATCCAGCTAGGGAATTCGTGCTGGGAGCTCTTCTGCCTGGAGCACGGCATTCAACCCAATGGAAAGGCGATCGATCGCAAgtaagcgcgt ... tctcttccagCGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTTTTTCAGCGAGGCGGCGTCCGCGACGAAGCACGTCCCAAGGGCGGTGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcttaatcccccgattgctcaaagttcccctcgaaatcttccttctcttccagCGATCACCAGGAAGCCATGGCCGGAGCTACCAAGGAATCGTTTGGAACCTTTTTCAGCGAGGCGGCGTCCGCGACGAAGCACGTCCCAAGGGCGGTGATG
  tcttaat  putative branch site (score: 10)
                          ttcccctcgaaatctt  putative PPT
                                   aaatctt  TA-rich tract