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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctctctctctctctctctctctctcccctttgatttgctgtagctctagtacttctttctaaaccgtttgtttttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAAAAGTGTTCTTA

Basic information

species Selaginella moellendorffii
transcript EFJ06917
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06917 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S99_158V6.1 (Physcomitrella patens), 3'ss of exon 12
--gtactctctctctctctctctctctctctcccctttgatttgctgtagctctagtacttctttctaaaccgt-ttgtt---tttgt-tggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAA--AAAGTGTTCTTA
      |   | ||| |   |      |  | ||||||  | |        | ||| |  | |||| |||  |  ||||      |||     | |  |||||||| || ||||||||||||||||  |||||||||||||| || ||||||||| | ||  | || |||||   ||| |  |  |    ||| |  | |  
aatcgtttgttttcttttcatgcaaggcgtttccctttattctctcacgaatatagaatatttttcaaaattgaattgtgaaacctgtgcacgtgattagGATTCTTGGAGATGTGTTCATGGGGGCTTACCATACGGTGTTCGACTTCGGGAACCAGCGATTGGGCTTCGCTTTGGCTGCTTAGATCCCAAAATAATAT--
















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|169053522|gb|FE461445.1|FE461445
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169025758|gb|FE433668.1|FE433668
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169058293|gb|FE466034.1|FE466034
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169048944|gb|FE456061.1|FE456061
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169112994|gb|FE515474.1|FE515474
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATCCCATTCGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169034781|gb|FE445634.1|FE445634
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169112989|gb|FE515469.1|FE515469
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169047466|gb|FE455661.1|FE455661
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169080225|gb|FE488904.1|FE488904
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169057176|gb|FE464687.1|FE464687
EST:     CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: CTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... 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: 80

TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCCTTAGTGGCTTTACAGGAATGGACGTCCCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAAAAGTGTTCTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctgtagctctagtacttctttctaaaccgtttgtttttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAAAAGTGTTCTTA
                       ttctaaa  putative branch site (score: 80)
                                 tttgttttt  TA-rich tract