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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgtgggaaactagagtttgtggtcctcatctgttctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGCAGCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ19479
intron # 3
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|169031850|gb|FE440134.1|FE440134
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169022993|gb|FE431567.1|FE431567
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCAGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169065530|gb|FE474822.1|FE474822
EST:     GAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCAGC
genomic: GAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169096827|gb|FE499843.1|FE499843
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169023007|gb|FE431568.1|FE431568
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCAGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169031877|gb|FE440135.1|FE440135
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169065531|gb|FE474823.1|FE474823
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCAGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169107720|gb|FE510936.1|FE510936
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCAGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC
EST: gi|169107719|gb|FE510935.1|FE510935
EST:     TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTAT                         ATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCAGC
genomic: TCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGC

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: 33 (upstream exon), 35 (downstream exon)
Score: 9

CTTTGAGTACTGGTCGTTCGAAACTCTCGTACTTCTTTCCGGAATTTTGCCCAACCCTCAACTTGAAACGTCAGCTTTCTCGATTATgtaagtttgt ... tctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGCAGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtttgtgggaaactagagtttgtggtcctcatctgttctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGCAGCAAG
                                      tcctcatctgttct  CT-rich tract
      taagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgtgggaaactagagtttgtggtcctcatctgttctgttgcagATTAAACACATTGTCTCTGTGCTATATGGTTCCTTATGGCCTGAGTGCGGCAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG