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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcgtctggatcgatggcgatgggagagggtttgatggtgggattttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTTGTCGCCGCCGAGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ22466
intron # 1
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|169046730|gb|FE456668.1|FE456668
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169070532|gb|FE479809.1|FE479809
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169019639|gb|FE427468.1|FE427468
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|70670894|gb|DN839471.1|DN839471
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169025044|gb|FE434670.1|FE434670
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169106951|gb|FE508834.1|FE508834
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169036088|gb|FE445128.1|FE445128
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169060729|gb|FE469755.1|FE469755
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169054265|gb|FE463206.1|FE463206
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169019638|gb|FE427467.1|FE427467
EST:     AGCGCGCATTCAAG                         GTGATTGCT-GGCTCAAC-ATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169068959|gb|FE477703.1|FE477703
EST:     AAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169048812|gb|FE455292.1|FE455292
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169099322|gb|FE502108.1|FE502108
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169044589|gb|FE450628.1|FE450628
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169042965|gb|FE452319.1|FE452319
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
EST: gi|169060728|gb|FE469754.1|FE469754
EST:     GATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGA-TGCTGGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGT
genomic: GATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCT-GGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGT
EST: gi|169027095|gb|FE435629.1|FE435629
EST:     AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAG                         GTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT
genomic: AATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTT

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: 53

ATCGTCCAGGCGCGGCACCGTTCGCGCGTCGTCCAGGTCCGCGGGAGGAGAATGCCGGGATTTTGCGCTCCGGGATGTCTTTGCGAAGCGCGCATTCAAGgtattcgtct ... tttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTTGTCGCCGCCGAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgtctggatcgatggcgatgggagagggtttgatggtgggattttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTTGTCGCCGCCGAGAAG
                              gtttgat  putative branch site (score: 53)
                                            ttttcttgc  putative PPT
                                           attttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcgtctggatcgatggcgatgggagagggtttgatggtgggattttcttgcagGTGATTGCTGGGCTCAACAATTTCGATCGAGAGAATGTGGCTGATGTGGTTGTCGCCGCCGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT