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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaaaaacgagttttttttttcctctctctcctgttttgcagaagcaaactaacgtgagattgtgtggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAGATCTCTGAGGGACAGGATATGGCTGCTTATAGCTCCTCCAAAGTTGTGG

Basic information

species Selaginella moellendorffii
transcript EFJ09286
intron # 5
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|70670289|gb|DN838866.1|DN838866
EST:     ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAGGGAGGAGCTAGACAAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169113664|gb|FE515290.1|FE515290
EST:     ACAATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGCAGCTAGACGAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169046274|gb|FE456407.1|FE456407
EST:     ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169081288|gb|FE489278.1|FE489278
EST:     ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169100903|gb|FE502233.1|FE502233
EST:     ACAATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGCAGCTAGACGAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169078884|gb|FE489656.1|FE489656
EST:     ACAATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGCAGCTAGACGAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169066576|gb|FE474136.1|FE474136
EST:     ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169115072|gb|FE516645.1|FE516645
EST:     ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169102736|gb|FE508091.1|FE508091
EST:     ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169045727|gb|FE451700.1|FE451700
EST:     ACAATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGCAGCTAGACGAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG
EST: gi|169045726|gb|FE451699.1|FE451699
EST:     ACAATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAG                         GATGGACTCCGGATCACTTATATGTGGATCAAGGAGCAGCTAGACGAGGAG
genomic: ACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAG

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: 21

AATCCACCATATCCCTGGGCCAGAAGGTGTTCGTGGTAGAAATTCGGACAACGATCTGATAAAGGAGAAGCTCGGTTGGGCCCCAACAATGCGACTCAAGgtgaaaaaac ... tggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAGATCTCTGAGGGACAGGATATGGCTGCTTATAGCTCCTCCAAAGTTGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctctctcctgttttgcagaagcaaactaacgtgagattgtgtggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAGATCTCTGAGGGACAGGATATGGCTGCTTATAGCTCCTCCAAAGTTGTGG
                           aactaac  putative branch site (score: 21)
                          aaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaaaaacgagttttttttttcctctctctcctgttttgcagaagcaaactaacgtgagattgtgtggtgtgtagGATGGACTCCGGATCACTTATATGTGGATCAAGGAGGAGCTAGACAAGGAGATCTCTGAGGGACAGGATATGGCTGCTTATAGCTCCTCCAAAGTTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC