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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgcttttttgctgtttgttttgcaagtgattaactgcgatgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCGATTGTTGACAGCCCTGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ17159
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|169065121|gb|FE474569.1|FE474569
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAAC
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAAC
EST: gi|169070813|gb|FE480649.1|FE480649
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
EST: gi|169081337|gb|FE488768.1|FE488768
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
EST: gi|169115457|gb|FE516198.1|FE516198
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
EST: gi|169088109|gb|FE493361.1|FE493361
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAA-TTCGCTACGGCG
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
EST: gi|169115458|gb|FE516199.1|FE516199
EST:     ANAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
EST: gi|169081338|gb|FE488769.1|FE488769
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
EST: gi|169088108|gb|FE493360.1|FE493360
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCG
EST: gi|169070814|gb|FE480650.1|FE480650
EST:     AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAAT                         GCTCTTGCTCT-GGNACATATGTTTCACGAGAGTAA
genomic: AAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGG-ACATATGTTTCACGAGAGTAA

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: 41

CTCAATCTTGAACGTTAACCCAGTCGATGTTGTTGCAAGGCATGTGGAACAAAAGCGGCACTGTCACAGTGAATTCGGAGCCGGACACTGGCAGAAGAATgtgagtcgct ... tgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCGATTGTTGACAGCCCTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtcgcttttttgctgtttgttttgcaagtgattaactgcgatgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCGATTGTTGACAGCCCTGAAG
                                 gattaac  putative branch site (score: 41)
                   tttgtttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgcttttttgctgtttgttttgcaagtgattaactgcgatgctgtgcagGCTCTTGCTCTTGGACATATGTTTCACGAGAGTAACAAATTCGCTACGGCGATTGTTGACAGCCCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG