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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttttcgtttggcacttgagaagactcgtgcttatggtttccttctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCGGTATGACTGGCGATGGTGTGAACGACGCTCCTGCGTTAAAGAAGGCAGA

Basic information

species Selaginella moellendorffii
transcript EFJ18860
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: EDP06054 (Chlamydomonas reinhardtii), 3'ss of exon 8
-----------------------------------------------------------------gtaaacttttcgtttggcacttgaga------------agactcgtgcttatggtttccttctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCGGTATGACTGGCGATGGTGTGAACGACGCTCCTGCGTTAAAGAAGGCAGA
                                                                 | |||  |   |  ||  |  |||||            | || ||     |||| |||    |||  |  || ||||||||    || ||| ||  |||||   | ||         |||||||||||| |||||||| ||||||||||| || ||  | |          
gtggggctgcattggtggtgtttgggtggcgctgtgcaacgcggtgatcgtacgcggcagcaagagcaaagctacggaatgaaaagtgagatatgctgagtcgacacccgattgcatggcttcagG-TGTACCCCGAGCACAAGTACCTGATCGTGGAGGCGCTGCGCCAGAACGGCTTCGCCTGCGGTATGACCGGCGATGGCGTGAACGACGCCCCCGCCCTGA----------

upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: EDP08073 (Chlamydomonas reinhardtii), 3'ss of exon 10
--------------gtaaacttttcgtttggcacttgagaagactcgtgcttatggtttccttctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCGGTATGACTGGCGATGGTGTGAACGACGCTCCTGCGTTAAAGAAGGCAGA--------------------------------
              |   |  |   |    |  |||     | |    |||   |||    |||||       | |       |    |||  |  ||    || ||     | ||  ||   || ||||| ||||| |||||||||||||| |||||| | |||||||| ||                                
gagctcaggcgcaggcggatctccgggcgtgtgctttctgggtcgt-cgctctcggtcaggttctgacctgccatccttctcctcccgttgccaccaa----cagGAGGCCGACCACGTCGTGGGCATGACCGGCGACGGTGTGAACGACGCGCCTGCGCTGAAGAAGGCCGATGTGGGTATCGCTGTGGCCGGCGCCACTGATG

upper sequence: EFJ18860 (Selaginella moellendorffii), 3'ss of exon 13
lower sequence: PP1S137_291V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------------------------------------------------------------gtaaacttttcgtttggcacttgagaagactcgtgc-ttatggtttccttctgtg-tctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCGGTATGACTGGCGATGGTGTGAACGACGCTCCTGCGTTAAAGAAGGCAGA
                                                                                               ||   |||  | | |  ||         |      || | |||   || | || |  ||||||||||||||||||||| |||| | | || ||||| || |||||    ||||||||||| |||||||| || || |||||||| || || ||||| ||
gtgagcttcattgattcagtatttgttcaaaactaaacatagaccaacatcatttgtatgaattttttttcttagcacagttctatgctcctaacaattcttttttctagtgctgctatttcttaccatattgttgttctgttgtatgatgcagAACACAAGTATGAAATTGTTAAGAGGTTACAGGAAAAAAAACATATTGTTGGTATGACTGGTGATGGTGTAAATGATGCTCCTGCTTTGAAAAAGGCCGA

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|169021094|gb|FE430703.1|FE430703
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169116091|gb|FE517454.1|FE517454
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169028222|gb|FE432188.1|FE432188
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169074592|gb|FE480874.1|FE480874
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169114143|gb|FE516822.1|FE516822
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169107442|gb|FE508311.1|FE508311
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169027081|gb|FE435615.1|FE435615
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169026011|gb|FE434454.1|FE434454
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169096134|gb|FE500294.1|FE500294
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169045923|gb|FE451233.1|FE451233
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169081472|gb|FE487733.1|FE487733
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169110944|gb|FE509856.1|FE509856
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169022707|gb|FE429734.1|FE429734
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169023502|gb|FE431920.1|FE431920
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169027227|gb|FE436125.1|FE436125
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169052201|gb|FE461411.1|FE461411
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169083022|gb|FE488544.1|FE488544
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169029737|gb|FE438344.1|FE438344
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169082644|gb|FE486203.1|FE486203
EST:     GGTTGAGGAGCTGATTGAAAAGGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
EST: gi|169028953|gb|FE438626.1|FE438626
EST:     GGTTGAGGAGCTGATTGANAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAA
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAA
EST: gi|169044104|gb|FE452106.1|FE452106
EST:     GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAG                         AACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG
genomic: GGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCG

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: 51

TCTTCTTCGCTGCTTGGAAACCACAAAGATGAGAATCTTGCTGCGCTTCCGGTTGAGGAGCTGATTGAAAAAGCTGATGGTTTTGCTGGAGTATTCCCAGgtaaactttt ... ctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCGGTATGACTGGCGATGGTGTGAACGACGCTCCTGCGTTAAAGAAGGCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttcgtttggcacttgagaagactcgtgcttatggtttccttctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCGGTATGACTGGCGATGGTGTGAACGACGCTCCTGCGTTAAAGAAGGCAGA
                                      tttccttctgtgtct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttttcgtttggcacttgagaagactcgtgcttatggtttccttctgtgtctagAACACAAGTATGAAATTGTGAAGAAGCTGCAAGAAAAGAAGCATATCTGCGGTATGACTGGCGATGGTGTGAACGACGCTCCTGCGTTAAAGAAGGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG