Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGGCAAGCGCGAGCTTATCGTTGGCAAAGACGACGAACTGCTGAACACTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacagctgagaaagtctagcactacttttgcttattcttttcttccaatcttctag

Basic information

species Selaginella moellendorffii
transcript EFJ29885
intron # 5
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|169107964|gb|FE513793.1|FE513793
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169050407|gb|FE457590.1|FE457590
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169058284|gb|FE465011.1|FE465011
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169050408|gb|FE457591.1|FE457591
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTC-AAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|70670825|gb|DN839402.1|DN839402
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169062142|gb|FE471034.1|FE471034
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169062143|gb|FE471035.1|FE471035
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169058285|gb|FE465012.1|FE465012
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169038255|gb|FE443941.1|FE443941
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169060860|gb|FE469255.1|FE469255
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169104935|gb|FE509053.1|FE509053
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169104934|gb|FE509052.1|FE509052
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAG
EST: gi|169107965|gb|FE513794.1|FE513794
EST:     CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAG                         GCTTTACTGCACGAGGAAGCCAAGAACAA-GCCTTTGATATTGCTTCCA
genomic: CTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCA

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: 118

AGGAGGCAAGCGCGAGCTTATCGTTGGCAAAGACGACGAACTGCTGAACACTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacag ... aatcttctagGCTTTACTGCACGAGGAAGCCAAGAACAAAGCCTTTGATATTGCTTCCAAGGCCGAAGAAGAAGGTTCGCCAACTACAGATTTTAAGAGCTTGTTCTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAGGCAAGCGCGAGCTTATCGTTGGCAAAGACGACGAACTGCTGAACACTAGCACCAAGAGCATCCCAAGAGAAGATGTGGCGGAAGTGTGCATCCAGgtactcacagctgagaaagtctagcactacttttgcttattcttttcttccaatcttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG