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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATGCGGCCATTGTAAGAATTATGAAGACTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctggctgctgttggaatgtggtgccgacgctggatatgttttttgtgtgtgaccag

Basic information

species Selaginella moellendorffii
transcript EFJ26297
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26297 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: AC177936.6_FGT008 (Zea mays), 5'ss of exon 4
ATTGATGCGGCCATTGTAAGAATTATGAAGACTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcct--ggctgctgttggaatgtggtgccgacgctggatatgttttttgtgtgtgaccag--------------------------------------
 ||||||||||||| ||  |||| ||||||||  |||||||||||||||||||  | || ||||| ||||| | ||| ||||| |  | |  |  |  |  |  | |  | ||   | | |   ||  ||         |||||                                        
GTTGATGCGGCCATAGTTCGAATAATGAAGACGCGGAAGGTCCTGAGCCACACCCTTCTAATAACCGAGCTTTACCAGCAGgtgacacttcagaatattaattaatttagctgtgtatgttatttaccttacgacaacttgaccccctttaacctttggggttcatccatgtctctcatttcag
















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|169052725|gb|FE461155.1|FE461155
EST:     CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169083877|gb|FE492789.1|FE492789
EST:     CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169077256|gb|FE485142.1|FE485142
EST:     CTAGGAAGGTCCTGAGCCACACGTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169078485|gb|FE488360.1|FE488360
EST:     CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169053211|gb|FE462486.1|FE462486
EST:     CTAGGAAGGTCCTGAGCCACACGTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169039037|gb|FE450443.1|FE450443
EST:     CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169078955|gb|FE487634.1|FE487634
EST:     CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169094797|gb|FE492948.1|FE492948
EST:     CTAGGAAGGTCCTGAGCCACACGTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169094958|gb|FE493005.1|FE493005
EST:     CTAGGAAGGTCCTGAGCCACACGTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
EST: gi|169039036|gb|FE450442.1|FE450442
EST:     CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAG                         CTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG
genomic: CTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTG

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: 34 (upstream exon), 35 (downstream exon)
Score: 16

ATTGATGCGGCCATTGTAAGAATTATGAAGACTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctg ... gtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATGCGGCCATTGTAAGAATTATGAAGACTAGGAAGGTCCTGAGCCACACTTTACTGATAACGGAGCTGTTCCAACAGgtaaggcctggctgctgttggaatgtggtgccgacgctggatatgttttttgtgtgtgaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT