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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttttttctttgtttcggccgagcttcttcttctcatctcgctcttgtaacttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCCTGCCAAGTCTTTCCGGATGAGAAAATCCTACTTCAACAACGAG

Basic information

species Selaginella moellendorffii
transcript EFJ16068
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|169103763|gb|FE506128.1|FE506128
EST:     AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATC                         GCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
genomic: AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATCgtgagttttt ... ttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
EST: gi|169054694|gb|FE461634.1|FE461634
EST:     AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATC                         GCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
genomic: AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATCgtgagttttt ... ttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
EST: gi|169102913|gb|FE505278.1|FE505278
EST:     AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATC                         GCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
genomic: AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATCgtgagttttt ... ttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
EST: gi|169078345|gb|FE490378.1|FE490378
EST:     AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATC                         GCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
genomic: AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATCgtgagttttt ... ttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
EST: gi|169076017|gb|FE480999.1|FE480999
EST:     AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATC                         GCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
genomic: AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATCgtgagttttt ... ttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
EST: gi|169070878|gb|FE480662.1|FE480662
EST:     AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATC                         GCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC
genomic: AAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATCgtgagttttt ... ttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCC

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), 35 (downstream exon)
Score: 28

CGCTGTCGCTGGTGATGGTTCTCATCGGCGTGCTGCGCCACTTCGTCTCCAAGTGTATGTCCTCGCAGCCGGAGCCCGACGCCAAGGCTCTCAAAGAATCgtgagttttt ... ttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCCTGCCAAGTCTTTCCGGATGAGAAAATCCTACTTCAACAACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgtttcggccgagcttcttcttctcatctcgctcttgtaacttccttcaagGCAAATTGTTCTTCGCGCCAGGTACCTGAGAGCGGCTGCGAATTACATTCCTGCCAAGTCTTTCCGGATGAGAAAATCCTACTTCAACAACGAG
                                      ttgtaac  putative branch site (score: 28)
                 cttcttcttctcatct  CT-rich tract