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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgaatggcttctttcaagggttcgttgatctacattcttccaagattttagtcttcatttgcatttctctaatgaattgtatttgcttgtgatttcagGTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGACATCAGTGGGTTATGGCTTAG

Basic information

species Physcomitrella patens
transcript PP1S128_91V6.1
intron # 11
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|37823041|gb|BJ581107.1|BJ581107
EST:     GGCTTGGGAGATATTCTGCTTCCAGGACTTTTAGTGTCCTTCTGCTTACG                         GTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGAC
genomic: GGCTTTGGAGATATTCTGCTTCCAGGACTTTTAGTGTCCTTCTGCTTACGgtatttccct ... gtgatttcagGTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGAC
EST: gi|37834514|gb|BJ592526.1|BJ592526
EST:     GGCTTTGGAGATATTCTGCTTCCAGGACTTTTAGTGTCCTTCTGCTTACG                         GTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGAC
genomic: GGCTTTGGAGATATTCTGCTTCCAGGACTTTTAGTGTCCTTCTGCTTACGgtatttccct ... gtgatttcagGTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGAC
EST: gi|208381949|gb|DC923822.1|DC923822
EST:     GGCTTTGGAGATATTCTGCTTCCAGGACTTTTAGTGTCCTTCTGCTTACG                         GTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGAC
genomic: GGCTTTGGAGATATTCTGCTTCCAGGACTTTTAGTGTCCTTCTGCTTACGgtatttccct ... gtgatttcagGTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGAC

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: 25 (upstream exon), 34 (downstream exon)
Score: 3

TTCTGAAAGTCCCCCGGTTGTATGACCCATGGGGTGGCTACAGCATCATCGGCTTTGGAGATATTCTGCTTCCAGGACTTTTAGTGTCCTTCTGCTTACGgtatttccct ... gtgatttcagGTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGACATCAGTGGGTTATGGCTTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttagtcttcatttgcatttctctaatgaattgtatttgcttgtgatttcagGTATGATTGGGTGTCGAAGAAGAGTCTTTTCAACGGGTACTTTTTGTGGACATCAGTGGGTTATGGCTTAG
                       ctctaat  putative branch site (score: 3)
                          taatgaattgtattt  TA-rich tract