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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttttttcgctcgtggcgtcgccgtgctaaaaatccgtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTACATCCTCTGGCTGCGCTACAGCTCCAAAGGCAAACGGGACCACGAGATT

Basic information

species Selaginella moellendorffii
transcript EFJ32436
intron # 8
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|169078281|gb|FE488884.1|FE488884
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169070700|gb|FE480627.1|FE480627
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169065936|gb|FE475384.1|FE475384
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169035439|gb|FE444377.1|FE444377
EST:     CCATTCAAGGCAGCAATGTTTNGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169113801|gb|FE515362.1|FE515362
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATGGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169035440|gb|FE444378.1|FE444378
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169033927|gb|FE441959.1|FE441959
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169081856|gb|FE490524.1|FE490524
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169020249|gb|FE428272.1|FE428272
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169081855|gb|FE490523.1|FE490523
EST:     TTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: TTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
EST: gi|169081181|gb|FE490783.1|FE490783
EST:     CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAG                         AGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA
genomic: CCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTA

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: 26

CTGCTGTAAACTTCGTAAATTGGCTTCAAGATGTCGCTTCATGGAGGGAGCCATTCAAGGCAGCAATGTTTTGTCTGCTCTTCTCGTATATATTTTATAGgtgagttttt ... gtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTACATCCTCTGGCTGCGCTACAGCTCCAAAGGCAAACGGGACCACGAGATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtttttttttcgctcgtggcgtcgccgtgctaaaaatccgtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTACATCCTCTGGCTGCGCTACAGCTCCAAAGGCAAACGGGACCACGAGATT
                                 tgctaaa  putative branch site (score: 26)
                                          tccgtcctt  putative PPT
     agttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttttttcgctcgtggcgtcgccgtgctaaaaatccgtccttgcagAGATTGGGTCCGATACCTTCCACCGCTTCTCCTCCTCGTCATCGTCTTGTACATCCTCTGGCTGCGCTACAGCTCCAAAGGCAAACGGGACCACGAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC