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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttctgactggatgattaccatcttaacttggactcaaatgctacttcctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTGTATAAGTGTTTACGAGACAGAGACCATGGGTTTACTGGACAAGAAGTCG

Basic information

species Selaginella moellendorffii
transcript EFJ12681
intron # 7
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|169028107|gb|FE435959.1|FE435959
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGANAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
EST: gi|169041301|gb|FE446844.1|FE446844
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
EST: gi|169087397|gb|FE492200.1|FE492200
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
EST: gi|169112795|gb|FE515171.1|FE515171
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
EST: gi|169030830|gb|FE436811.1|FE436811
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
EST: gi|169055815|gb|FE466707.1|FE466707
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
EST: gi|169027755|gb|FE434567.1|FE434567
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
EST: gi|169030052|gb|FE440518.1|FE440518
EST:     GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAG                         GTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG
genomic: GCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTG

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: 46

TACGAAGTGGTAAATCGCACCGAGAATTCAAGGGCAGCGCCGACGAGTTTGCTACTGGTGGGACTGGAGGTGTTGCCGGAGTGTCTTGGCCAGTGTTCAGgttagttctg ... ctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTGTATAAGTGTTTACGAGACAGAGACCATGGGTTTACTGGACAAGAAGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactggatgattaccatcttaacttggactcaaatgctacttcctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTGTATAAGTGTTTACGAGACAGAGACCATGGGTTTACTGGACAAGAAGTCG
                  tcttaac  putative branch site (score: 46)
                                      ctacttcct  putative PPT
        atgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttctgactggatgattaccatcttaacttggactcaaatgctacttcctacatctagGTGGTCTGGCGGCCGTGATGACAAGTATTTTGCGCGTATAGGAAAGCACTGTATAAGTGTTTACGAGACAGAGACCATGGGTTTACTGGACAAGAAGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT