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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaactctaagcaaagagtttcaatggctcgcgagctaaaagtcgtgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAACGTCGGCTACGGCAAGGAAGACGGCAAGGCTTACTGGATCATCAAAAACT

Basic information

species Selaginella moellendorffii
transcript EFJ36576
intron # 3
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|169071628|gb|FE476563.1|FE476563
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169069378|gb|FE479474.1|FE479474
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169068391|gb|FE478981.1|FE478981
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|70670447|gb|DN839024.1|DN839024
EST:     TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGGGAAGTGTGGGAACCCGAC-TCGACCACGGTGTGACC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGG-AGGTGTGG-AACC-GACCTCGACCACGGTGTGACC
EST: gi|169107395|gb|FE504169.1|FE504169
EST:     TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169111577|gb|FE511867.1|FE511867
EST:     TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169020788|gb|FE430189.1|FE430189
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169068392|gb|FE478982.1|FE478982
EST:     AGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: AGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169071994|gb|FE477683.1|FE477683
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169111578|gb|FE511868.1|FE511868
EST:     TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169069754|gb|FE478303.1|FE478303
EST:     TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169109484|gb|FE514130.1|FE514130
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169040444|gb|FE448444.1|FE448444
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169111834|gb|FE511214.1|FE511214
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169060244|gb|FE467606.1|FE467606
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC
EST: gi|169058162|gb|FE466592.1|FE466592
EST:     TGAGCGTAGCCATCGACGCCGGTGGCTCGAGCATGCAGTTCTACAGATCG                         GGAATTTTCACTGGCACGTGTGGAACCGACCTCGACCACTGTGTGACCAAC
genomic: TGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAAC

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: 152

TCCAGTGAACGATGAGACAGCGCTCTTGAAAGCCGTGGCTCATCAGCCCGTGAGCGTAGCCATCGACGCGGGTGGCTCGAGCATGCAGTTCTACAGATCGgtgagtaaac ... tgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAACGTCGGCTACGGCAAGGAAGACGGCAAGGCTTACTGGATCATCAAAAACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaactctaagcaaagagtttcaatggctcgcgagctaaaagtcgtgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAACGTCGGCTACGGCAAGGAAGACGGCAAGGCTTACTGGATCATCAAAAACT
                                 agctaaa  putative branch site (score: 152)
                  tttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaaactctaagcaaagagtttcaatggctcgcgagctaaaagtcgtgatttgcagGGAATTTTCACTGGGAGGTGTGGAACCGACCTCGACCACGGTGTGACCAACGTCGGCTACGGCAAGGAAGACGGCAAGGCTTACTGGATCATCAAAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA