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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtagccaatctgactacactctcggacattttgactgcctagcggagttctagttcctaaatggcatctaagttctgtctcggttactcttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG

Basic information

species Physcomitrella patens
transcript PP1S109_70V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S109_70V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgtagccaatctgactacactctcggacattttgactgcctagcggagttctagttcctaaatggcatctaagttctgtctcggttactcttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG
  |||   |||    | |     || || | |   | ||| |  ||   ||   |||  |   | | ||| ||| |    || | ||  | ||  | |||||||||||||||| ||| | || |||||||||||||||||||| ||||  || ||||    ||||||||  ||||   | || ||||
--gtaattaattaatcgat----tcagatact---aatgcttttcga--tttaggttttt---ttgaatcgaagcttgagcttgatt--tgtttctgcagTGCATTACACTGGAACTTTGCTTGATGGGACGAAGTTTGATTCGAGTCGTGATAGAGCAACGCCTTTCAAATTCACTCTTGGACAAG
















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|208368642|gb|DC940021.1|DC940021
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|100365372|gb|BY966565.1|BY966565
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|162221593|gb|FC397610.1|FC397610
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|100447939|gb|CJ972238.1|CJ972238
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|67570816|gb|BJ943640.1|BJ943640
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|67573557|gb|BJ946381.1|BJ946381
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|162173905|gb|FC349705.1|FC349705
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|18360372|gb|BJ192434.1|BJ192434
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|67716695|gb|BJ966955.1|BJ966955
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|162193217|gb|FC371524.1|FC371524
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
EST: gi|100362283|gb|BY947282.1|BY947282
EST:     CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAG                         TGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG
genomic: CAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGG

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: 32 (upstream exon), 27 (downstream exon)
Score: 31

GGGAAGGTTCAAGAATTGATCAAGGGCGGAGGGTTGCAAAAGCTTATTACCAAAGCTGGAGAAGGGTGGGAGACCCCTGATACTGGCGATGAAGTCTCAGgttagcatac ... cttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagttctagttcctaaatggcatctaagttctgtctcggttactcttgtttcagTGCATTACACTGGGACTCTACTCGATGGGACGAAGTTTGATTCAAGTCTGGACAGAGGGCAGCCTTTCACCTTCAAATTGGGTCAAG
           tcctaaa  putative branch site (score: 31)
                                           ctcttgtttc  putative PPT
              taaat  TA-rich tract