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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccgatcattcaaggactcttccgttgaagcttttttcag

Basic information

species Selaginella moellendorffii
transcript EFJ22768
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|169028104|gb|FE435956.1|FE435956
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169096681|gb|FE496811.1|FE496811
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169081666|gb|FE491320.1|FE491320
EST:     AGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTTCGAACAATGGGGGATGCTGGCAGGACA
genomic: AGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169109250|gb|FE510230.1|FE510230
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169096537|gb|FE499449.1|FE499449
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169082427|gb|FE488989.1|FE488989
EST:     TCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169075666|gb|FE482052.1|FE482052
EST:     TCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169031591|gb|FE439056.1|FE439056
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169080525|gb|FE488463.1|FE488463
EST:     CGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: CGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169028103|gb|FE435955.1|FE435955
EST:     ACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: ACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169096682|gb|FE496812.1|FE496812
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169026482|gb|FE434769.1|FE434769
EST:     GAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: GAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169096538|gb|FE499450.1|FE499450
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169083003|gb|FE488525.1|FE488525
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169050286|gb|FE458353.1|FE458353
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169081076|gb|FE486141.1|FE486141
EST:     TGTTCGGGTTTTCCA-GAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTAC
genomic: TGTTCGGGTTT-CCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTAC
EST: gi|169114821|gb|FE516082.1|FE516082
EST:     TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: TTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
EST: gi|169080940|gb|FE486109.1|FE486109
EST:     GTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG                         ATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA
genomic: GTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACA

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: 61

GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccg ... cttttttcagATATGCAAACAAACGAATGCCTTACGAACAATGGGGGATGCTGGCAGGACAAGAGCGCGAACGTCACCGCATGTAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAGgtagattccgatcattcaaggactcttccgttgaagcttttttcag

- - - - - - - - - - - - - - - - - - - - - - - - AAGAAA