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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctaaaattacatggaatctatcacgtctaatgcctattgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT

Basic information

species Selaginella moellendorffii
transcript EFJ11288
intron # 16
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:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169069767|gb|FE477484.1|FE477484
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169093165|gb|FE494198.1|FE494198
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169081724|gb|FE488182.1|FE488182
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169077287|gb|FE485589.1|FE485589
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169052446|gb|FE462774.1|FE462774
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169076148|gb|FE485178.1|FE485178
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169029149|gb|FE439381.1|FE439381
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169096989|gb|FE500057.1|FE500057
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169044598|gb|FE450637.1|FE450637
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169040870|gb|FE447921.1|FE447921
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACCAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169020101|gb|FE430880.1|FE430880
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169096955|gb|FE497592.1|FE497592
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169096954|gb|FE497591.1|FE497591
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169078532|gb|FE490669.1|FE490669
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169028495|gb|FE439104.1|FE439104
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169066803|gb|FE473635.1|FE473635
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169029649|gb|FE437320.1|FE437320
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169033716|gb|FE441644.1|FE441644
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
EST: gi|169110787|gb|FE512637.1|FE512637
EST:     GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCT                         GTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA
genomic: GAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGA

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: 34 (upstream exon), 35 (downstream exon)
Score: 181

CTACCCCCTCAATGATACCGCTGCTACAATCAATGAGCTAGGCGGGACTATAAGGAGAGTGATGGGTGGCACTAGCGGTGTTCTgtgagttcta ... attgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagttctaaaattacatggaatctatcacgtctaatgcctattgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT
             ttctaaaattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctaaaattacatggaatctatcacgtctaatgcctattgttgcagGTATGACATATTCTCCAAGGCAGCGTATGTAAAGTTGAAGGACAACGCAGACCAGCCATTGACTGCCAAATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG