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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAAAGCTCATTGCAGCCGCCAAACCAGAATCACCCCCTGGCCAAGATCAAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtttctttgacaggcctcgtgcagttttacatttctgtttctttacttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ33842
intron # 19
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|169056743|gb|FE463916.1|FE463916
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169107553|gb|FE511718.1|FE511718
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169055550|gb|FE464583.1|FE464583
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGCTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169099786|gb|FE500791.1|FE500791
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169068100|gb|FE477390.1|FE477390
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169072954|gb|FE480809.1|FE480809
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169038685|gb|FE450156.1|FE450156
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169047424|gb|FE457492.1|FE457492
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169031178|gb|FE440383.1|FE440383
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
EST: gi|169082975|gb|FE488497.1|FE488497
EST:     AAAAGTACCATGCTCTTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCCACCGGAAAAACATTCCAACAACTTATCG
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCG
EST: gi|169112334|gb|FE512910.1|FE512910
EST:     AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAG                         AAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA
genomic: AAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACA

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), 34 (downstream exon)
Score: 28

GCTAAAGCTCATTGCAGCCGCCAAACCAGAATCACCCCCTGGCCAAGATCAAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtt ... ttacttgcagAAAGCAACCGGGAAAACATTCCAACAACTTATCGAAGAAGCGTTTGTTACACCGCTGAAGGTTACTGGCGAGTTTTACGTCGGCATTCCTCCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAAAGCTCATTGCAGCCGCCAAACCAGAATCACCCCCTGGCCAAGATCAAATGTACCATGGTCGTTCTTTTGGATGGATATGCGGTGGGATAGCTGAGgtacgacgtttctttgacaggcctcgtgcagttttacatttctgtttctttacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA