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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgctctctcatatattcatttttcactctctctctctctcccccttttaatttgctctagtacttctttctaaaacgtttggttttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAAAAGTGTTCTTA

Basic information

species Selaginella moellendorffii
transcript EFJ34434
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34434 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S99_158V6.1 (Physcomitrella patens), 3'ss of exon 12
--tcgctctctcatatattcatttttcactctctctctctctcccccttttaatttgctctagtacttctttctaaaacgtttggttttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAA--AAAGTGTTCTTA
  ||| |   |  | | |||||      |  | || || | | | |     ||| |    || |  |      | ||  ||      |       | |  |||||||| || ||||||||||||||||  |||||||||||||| || ||||||||| | ||  | || |||||   ||| |  |  |    ||| |  | |  
aatcgtttgttt-tcttttcatgcaaggcgtt-tccctttattctctcacgaatatagaatatttttcaaaattgaattgtgaaacctgtgcacgtgattagGATTCTTGGAGATGTGTTCATGGGGGCTTACCATACGGTGTTCGACTTCGGGAACCAGCGATTGGGCTTCGCTTTGGCTGCTTAGATCCCAAAATAATAT--
















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|169031797|gb|FE438482.1|FE438482
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169031872|gb|FE438505.1|FE438505
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169112151|gb|FE513494.1|FE513494
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169095717|gb|FE498876.1|FE498876
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169060203|gb|FE467565.1|FE467565
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169110929|gb|FE509334.1|FE509334
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169058238|gb|FE466005.1|FE466005
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169031935|gb|FE440661.1|FE440661
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169114468|gb|FE516538.1|FE516538
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169065200|gb|FE474024.1|FE474024
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169040181|gb|FE448948.1|FE448948
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169021618|gb|FE432137.1|FE432137
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169096045|gb|FE500023.1|FE500023
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169093446|gb|FE495727.1|FE495727
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169039672|gb|FE448606.1|FE448606
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169044448|gb|FE451072.1|FE451072
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169021619|gb|FE432138.1|FE432138
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGNGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169021385|gb|FE431176.1|FE431176
EST:     ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG

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: 155

TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAAAAGTGTTCTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatttgctctagtacttctttctaaaacgtttggttttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAAAAGTGTTCTTA
                       ttctaaa  putative branch site (score: 155)
                      tttctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgctctctcatatattcatttttcactctctctctctctcccccttttaatttgctctagtacttctttctaaaacgtttggttttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAAAAGTGTTCTTA

- -ctctctc
- - - - - - - - - -tttttca
- - - - - - - - - - - - - -tctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - gctctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtt