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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGTTGGCATTTTGCAAATTCATGGTCAAGCCTTCGACTTTGCTCGTACTGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagctaatcgtgccttgaggaccggcagtaacgagctgatggttttccaactcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ10635
intron # 6
splice site 5'
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|169115175|gb|FE515604.1|FE515604
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169026960|gb|FE434272.1|FE434272
EST:     TGGACGAGCCTACAAACCACCTTGACATTCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169028378|gb|FE439897.1|FE439897
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169052592|gb|FE461659.1|FE461659
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169036614|gb|FE444159.1|FE444159
EST:     TGGACGAGCCTACAAACCACCTTGACATTCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169054986|gb|FE462927.1|FE462927
EST:     TGGACGAGCCTACAAACCACCTTGACATTCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169078769|gb|FE489619.1|FE489619
EST:     TGGACGAGCCTACAAACCACCTTGACATTCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169105691|gb|FE508457.1|FE508457
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTGGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169027273|gb|FE436145.1|FE436145
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169026779|gb|FE436353.1|FE436353
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169116429|gb|FE518195.1|FE518195
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169080652|gb|FE487173.1|FE487173
EST:     TGGACGAGCCTACAAACCACCTTGACATTCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169087542|gb|FE494633.1|FE494633
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169056802|gb|FE465405.1|FE465405
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169027733|gb|FE433219.1|FE433219
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
EST: gi|169075650|gb|FE482036.1|FE482036
EST:     TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAG                         GAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC
genomic: TGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGC

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: 31 (upstream exon), 35 (downstream exon)
Score: 34

TCGGTTGGCATTTTGCAAATTCATGGTCAAGCCTTCGACTTTGCTCGTACTGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagc ... caactcgcagGAGGCTCTGAGAGAATACCACGGCACGGTTCTCGTCGTCTCGCACGATCGCTACTTTGTGCGGCAGATTGTCAACAGAGTCGTGGAAGTGAAGAACGGAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGTTGGCATTTTGCAAATTCATGGTCAAGCCTTCGACTTTGCTCGTACTGGACGAGCCTACAAACCACCTTGACATCCCTACGAAAGAAATGCTGGAGgtatgaaagctaatcgtgccttgaggaccggcagtaacgagctgatggttttccaactcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA