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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaacttgtagcatgattctgtgcgtcatcagcatgactgtgttctttgcatccaaattactaattgtcgactaactattcatgacctgtcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGTAGGGAGACTCTGGACATTTTGGCTTCTGAAACTGGGTTTGAACTTGAGA

Basic information

species Physcomitrella patens
transcript PP1S480_2V6.1
intron # 4
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|162182457|gb|FC358056.1|FC358056
EST:     AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAG                         AGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
genomic: AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAGgtgggaattg ... tcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
EST: gi|162265245|gb|FC440168.1|FC440168
EST:     AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAG                         AGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTGGGT
genomic: AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAGgtgggaattg ... tcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
EST: gi|100417890|gb|BY993235.1|BY993235
EST:     AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAG                         AGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
genomic: AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAGgtgggaattg ... tcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
EST: gi|162186993|gb|FC363399.1|FC363399
EST:     AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAG                         AGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
genomic: AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAGgtgggaattg ... tcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
EST: gi|100356913|gb|BY965342.1|BY965342
EST:     AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAG                         AGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
genomic: AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAGgtgggaattg ... tcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
EST: gi|162196722|gb|FC374661.1|FC374661
EST:     AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAG                         AGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT
genomic: AGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAGgtgggaattg ... tcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGT

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: 27 (upstream exon), 34 (downstream exon)
Score: 8

GTTGGAGAATACGACCTTACACCAAGGCGGAGTTCTTCCACCAAATCTCCTCCAGgtgggaattg ... tcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGTAGGGAGACTCTGGACATTTTGGCTTCTGAAACTGGGTTTGAACTTGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgcatccaaattactaattgtcgactaactattcatgacctgtcgattttagAGTGGCAAAGAACTTACAGTGAAGGGCATACGCGCCTTGGAGTATGTTGGTAGGGAGACTCTGGACATTTTGGCTTCTGAAACTGGGTTTGAACTTGAGA
                         gactaac  putative branch site (score: 8)
          aaattactaattgt  TA-rich tract