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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgaaggatacgaagaggttggtttgagaaggcttttttagcttatgagttgtgctgataatttgagctaacaatttccacttgggtggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGCTGCGAAACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGG

Basic information

species Physcomitrella patens
transcript PP1S49_243V6.1
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|208351044|gb|DC910507.1|DC910507
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|208374301|gb|DC941142.1|DC941142
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|100388850|gb|BY988726.1|BY988726
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|100362161|gb|BY947220.1|BY947220
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|208348263|gb|DC905505.1|DC905505
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|208344391|gb|DC912750.1|DC912750
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|208379070|gb|DC911595.1|DC911595
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|67573240|gb|BJ946064.1|BJ946064
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|162221894|gb|FC398162.1|FC398162
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|208379038|gb|DC907787.1|DC907787
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
EST: gi|208392456|gb|DC904274.1|DC904274
EST:     CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAG                         AGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC
genomic: CAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGC

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), 33 (downstream exon)
Score: 10

AGATCTTTGCGTTGAGTAGCAACGATTTCAGGAATGGAACCAACATTGTGCTTGATGGAGTACCGTGGAGGGTGCAAGgtacaatgaa ... ggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGCTGCGAAACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgagttgtgctgataatttgagctaacaatttccacttgggtggtggttaagAGTTTTTGCACGTGAAGCCCGGCAAGGGAGCAGCGTTTGTTCGTACCAAGCTGCGAAACTATATCACTGGCAACACAGTTGATCGTACTTTCCGAGCGGG
                       agctaac  putative branch site (score: 10)
             tgataattt  TA-rich tract