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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcttctcgctgatgtatgtgtttactcaaatgcaaacacgctttcgttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAGCTTCGGCAGGACACAGAACCATGCTTGATGCGTTGCTGCCTGCAGCAGC

Basic information

species Selaginella moellendorffii
transcript EFJ11288
intron # 17
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|169078093|gb|FE488787.1|FE488787
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169069767|gb|FE477484.1|FE477484
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169096076|gb|FE497363.1|FE497363
EST:     GTATGTAAAG-TGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169093165|gb|FE494198.1|FE494198
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169081724|gb|FE488182.1|FE488182
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169077287|gb|FE485589.1|FE485589
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169052446|gb|FE462774.1|FE462774
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169076148|gb|FE485178.1|FE485178
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169029149|gb|FE439381.1|FE439381
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169096989|gb|FE500057.1|FE500057
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169044598|gb|FE450637.1|FE450637
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169040870|gb|FE447921.1|FE447921
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169020101|gb|FE430880.1|FE430880
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169096955|gb|FE497592.1|FE497592
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169096954|gb|FE497591.1|FE497591
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169078532|gb|FE490669.1|FE490669
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACGTACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169028495|gb|FE439104.1|FE439104
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169066803|gb|FE473635.1|FE473635
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169029649|gb|FE437320.1|FE437320
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169033716|gb|FE441644.1|FE441644
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
EST: gi|169110787|gb|FE512637.1|FE512637
EST:     GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT                         GGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG
genomic: GTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAG

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: 206

GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCTgtgagtttct ... gttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAGCTTCGGCAGGACACAGAACCATGCTTGATGCGTTGCTGCCTGCAGCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctcgctgatgtatgtgtttactcaaatgcaaacacgctttcgttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAGCTTCGGCAGGACACAGAACCATGCTTGATGCGTTGCTGCCTGCAGCAGC
      cgctgat  putative branch site (score: 206)
                                        ctttcgtt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttcttctcgctgatgtatgtgtttactcaaatgcaaacacgctttcgttgtttcagGGAGCGATGCTCTTGATGCTGCCGTTACCGCTGTGAGTACATACGGCGGAGCTTCGGCAGGACACAGAACCATGCTTGATGCGTTGCTGCCTGCAGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG