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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcccgtttcaacttggtttacttggttgcactgattctagtcatgccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCCTCGTGTGTGGGCCTTCCACTCTCCAGACAAGCGTTGCGGAAGAATGCAG

Basic information

species Selaginella moellendorffii
transcript EFJ09843
intron # 7
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|169036588|gb|FE444146.1|FE444146
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169029979|gb|FE440497.1|FE440497
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCGCGAAGAAGTGGTCGGGGATCAACGTGGGGGTTC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169021647|gb|FE428864.1|FE428864
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCGCGAAGAAGTGGTCGGGGATCAACGTGGGGGTTC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169025224|gb|FE434135.1|FE434135
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169114117|gb|FE516796.1|FE516796
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169025986|gb|FE435274.1|FE435274
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169083132|gb|FE496428.1|FE496428
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169059648|gb|FE468882.1|FE468882
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169109120|gb|FE511322.1|FE511322
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169083133|gb|FE496429.1|FE496429
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169020671|gb|FE428837.1|FE428837
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCGCGAAGAAGTGGTCGGGGATCAACGTGGGGGTTC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169061544|gb|FE469331.1|FE469331
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169033039|gb|FE441373.1|FE441373
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169088445|gb|FE495491.1|FE495491
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCGCGAAGAAGTGGTCGGGGATCAACGTGGGGGTTC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169032375|gb|FE440932.1|FE440932
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCGCGAAGAAGTGGTCGGGGATCAACGTGGGGGTTC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169099716|gb|FE503113.1|FE503113
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCCGGTTT
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCC-GGTTT
EST: gi|169030873|gb|FE440312.1|FE440312
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169044967|gb|FE452735.1|FE452735
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169023053|gb|FE428715.1|FE428715
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169050958|gb|FE458128.1|FE458128
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169078749|gb|FE486531.1|FE486531
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169050959|gb|FE458129.1|FE458129
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169083575|gb|FE495360.1|FE495360
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
EST: gi|169087053|gb|FE493078.1|FE493078
EST:     TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAG                         AAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC
genomic: TCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCC

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: 26

GCTACCGGTGCCGGGGACAAAGTTGGAGTGGCAGGCTGTCAGCAGCACAGTCTCGTTGGGCCGTGGAACACCGTCTATGGAAACCGGCCTGAGCTTAAAGgtacgcccgt ... ccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCCTCGTGTGTGGGCCTTCCACTCTCCAGACAAGCGTTGCGGAAGAATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccgtttcaacttggtttacttggttgcactgattctagtcatgccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCCTCGTGTGTGGGCCTTCCACTCTCCAGACAAGCGTTGCGGAAGAATGCAG
                            cactgat  putative branch site (score: 26)
                                             ccacttcc  putative PPT
                tttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcccgtttcaacttggtttacttggttgcactgattctagtcatgccacttccagAAATCTTTGCCGGTTTCACGAAGAAGTGGTCGGGGATCAACGTGGGGGTCCTCGTGTGTGGGCCTTCCACTCTCCAGACAAGCGTTGCGGAAGAATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA