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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccattacagttctttttgttacagcagagtttagcgcttcatgatctgctttgaggtttgtcatgaacgtgaaatgttctcacaactcataattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGTGTCTAAGCCTTTACGTTACTACAGCAACAATTTAGTTAGCACCATAAAT

Basic information

species Physcomitrella patens
transcript PP1S221_46V6.1
intron # 2
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|208386361|gb|DC932857.1|DC932857
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|208362654|gb|DC931047.1|DC931047
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|208389985|gb|DC938040.1|DC938040
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|208369068|gb|DC931639.1|DC931639
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|208362659|gb|DC931052.1|DC931052
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|208361781|gb|DC935021.1|DC935021
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|100433963|gb|BY978901.1|BY978901
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|100386844|gb|BY988113.1|BY988113
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|208389039|gb|DC937372.1|DC937372
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
EST: gi|100418818|gb|BY975754.1|BY975754
EST:     GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAG                         GTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT
genomic: GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGT

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), 16 (downstream exon)
Score: 2

GGGGACCTGTGCAAGGTGGACGACATACAGAAGGTGTTCAAGCTTTACAGgtttggcttg ... taattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGTGTCTAAGCCTTTACGTTACTACAGCAACAATTTAGTTAGCACCATAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgctttgaggtttgtcatgaacgtgaaatgttctcacaactcataattggcagGTTTGAGGCTGTCATTCACTTCGCGGGTCTGAAGGCTGTGGGAGAAAGTGTGTCTAAGCCTTTACGTTACTACAGCAACAATTTAGTTAGCACCATAAAT
                                ttctcac  putative branch site (score: 2)
                                          tcataatt  TA-rich tract