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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtagcacgaatctttactgaagttatagctgatattatttgcctgtgtatggtcgctacaatcttttacttgcattgcttatttcaagattctcatttccatgagggaactctgaaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTCTTCCAGTCATTGATAAATGACAGCGTTAGTGCACTGTTTCCTCAAATGG

Basic information

species Physcomitrella patens
transcript PP1S58_188V6.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_188V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ26575 (Selaginella moellendorffii), 3'ss of exon 12
gtgtgtagcacgaatctttactgaagttatagctgatattatttgcctgtgtatggtcgctacaatcttttacttgcattgcttatttcaagattctcatttccatgagggaactctgaaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTCTTCCAGTCATTGATAAATGACAGCGTTAGTGCACTGTTTCCTCAAATGG
                                                            |||  ||      |    || |   |    || ||||   ||   |                 | ||||| |||||||| ||||| || ||| |||| |||||||| || || |||||||||||| |  | ||||| ||||| || |||||  |||||||||| ||||
---------------------------------------------------------gtataccctcgcccgttcatctttccggtactgagcttctttgttttgtt----------------ttcagCTTCAAGAAAAGTTCCGCCTCGACCTGGATGACGAAGAAGCCGTTCAGTTCTTCCAGACGCTCATAAACGACAGTGTCAGTGCGTTGTTTCCTCAGATGG

upper sequence: PP1S58_188V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ14829 (Selaginella moellendorffii), 3'ss of exon 13
gtgtgtagcacgaatctttactgaagttatagctgatattatttgcctgtgtatggtcgctacaatcttttacttgcattgcttatttcaagattctcatttccatgagggaactc-tgaaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTCTTCCAGTCATTGATAAATGACAGCGTTAGTGCACTGTTTCCTCAAATGG
                                                                          | |  |      ||||   |||   |     ||||    ||| |      | ||||| |||||||| ||||| || ||| |||| |||||||| || || |||||||||||| |  | ||||| ||||| || |||||  |||||||||| ||||
-----------------------------------------------------------------------gtataccctcgcccgttcatctttccggtac---tgagcttgctcgttttgttttcagCTTCAAGAAAAGTTCCGCCTCGACCTGGATGACGAAGAAGCCGTTCAGTTCTTCCAGACGCTCATAAACGACAGTGTCAGTGCGTTGTTTCCTCAGATGG
















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|37839893|gb|BJ597901.1|BJ597901
EST:     GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAG                         CTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
genomic: GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAGgtgtgtagca ... aaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
EST: gi|208363690|gb|DC954661.1|DC954661
EST:     GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAG                         CTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
genomic: GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAGgtgtgtagca ... aaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
EST: gi|37844231|gb|BJ602239.1|BJ602239
EST:     GAGCTANCATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAG                         CTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
genomic: GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAGgtgtgtagca ... aaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
EST: gi|208362375|gb|DC954621.1|DC954621
EST:     GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAG                         CTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
genomic: GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAGgtgtgtagca ... aaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
EST: gi|67697479|gb|BJ957712.1|BJ957712
EST:     GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAG                         CTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
genomic: GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAGgtgtgtagca ... aaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
EST: gi|162233433|gb|FC409918.1|FC409918
EST:     GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAG                         CTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC
genomic: GAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAGgtgtgtagca ... aaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTC

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: 12 (upstream exon), 24 (downstream exon)
Score: 1

TCTCAGGAAATCCAGTAATCTCATCCTGAATCTGTTTTATCTAATGGCTGGAGCTAACATCCCCGACATTGCTTCTGATCCTGAGAAGGGAATTTTGAAGgtgtgtagca ... aaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTCTTCCAGTCATTGATAAATGACAGCGTTAGTGCACTGTTTCCTCAAATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcattgcttatttcaagattctcatttccatgagggaactctgaaaagtgcagCTACAAGAAAAATTCCGGCTGGACTTGGACGACGAAGAGGCTGTGCAGTTCTTCCAGTCATTGATAAATGACAGCGTTAGTGCACTGTTTCCTCAAATGG
         ttatttcaa  TA-rich tract