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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggaatcccaatccaagttttttttttccaatcctttttttttttttttttgagtgtgtgtgctgatccttattctgttttgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGTATCTAAGCAGAGAGAGGAAGAGCGGCGAAGAACGCTCTACTGGAATGTG

Basic information

species Selaginella moellendorffii
transcript EFJ33020
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|169112068|gb|FE510720.1|FE510720
EST:     ATTGTACAGACCGCACTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169059929|gb|FE467291.1|FE467291
EST:     ATTGTACAGACCGCACTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169046459|gb|FE454746.1|FE454746
EST:     ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169111123|gb|FE509372.1|FE509372
EST:     ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAG
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAG
EST: gi|169036709|gb|FE444930.1|FE444930
EST:     ATTGTACAGACCGCACTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169051949|gb|FE460080.1|FE460080
EST:     ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169112069|gb|FE510721.1|FE510721
EST:     ATTGTACAGACCGCACTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169111122|gb|FE509371.1|FE509371
EST:     ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169046473|gb|FE454747.1|FE454747
EST:     ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169064230|gb|FE471585.1|FE471585
EST:     ATTGTACAGACCGCACTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTNNCT-GA-CGTAGATTCTT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTT--CTTGAACGTAGATTCTT
EST: gi|169103528|gb|FE507596.1|FE507596
EST:     ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169059930|gb|FE467292.1|FE467292
EST:     ATTGTACAGACCGCACTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
EST: gi|169053108|gb|FE463007.1|FE463007
EST:     ATTGTACAGACCGCACTGTATGCGGACTTCTTTTACTATTACATCAAGTG                         CTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT
genomic: ATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGT

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: 33 (upstream exon), 34 (downstream exon)
Score: 25

CATGGATATCTGGAATTGTACAGACCGCGCTGTATGCGGACTTCTTTTACTATTACATCAAGTGgtacggaatc ... tgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGTATCTAAGCAGAGAGAGGAAGAGCGGCGAAGAACGCTCTACTGGAATGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttttttttgagtgtgtgtgctgatccttattctgttttgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGTATCTAAGCAGAGAGAGGAAGAGCGGCGAAGAACGCTCTACTGGAATGTG
                         tgctgat  putative branch site (score: 25)
                               tccttattctgtttt  CT-rich tract
     tttttttttttgagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggaatcccaatccaagttttttttttccaatcctttttttttttttttttgagtgtgtgtgctgatccttattctgttttgcgttgcagCTGGAGGAACAACGAGAAGCTTCATCTTCCTTCTTGAACGTAGATTCTTGTATCTAAGCAGAGAGAGGAAGAGCGGCGAAGAACGCTCTACTGGAATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC