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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgtggttaatctttgccagtttatattattgcagcctcgcaagtagccggtgatagtattccaggcctttctaaaacttaaagattcgggatgcagtttctgatcgtgtggttttatctttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAAGACCGTTCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCT

Basic information

species Physcomitrella patens
transcript PP1S15_262V6.1
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|18359086|gb|BJ191146.1|BJ191146
EST:     TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACG                         CACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
genomic: TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACGgtatgcgtgg ... ttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
EST: gi|18356452|gb|BJ188511.1|BJ188511
EST:     TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACG                         CACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
genomic: TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACGgtatgcgtgg ... ttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
EST: gi|208348349|gb|DC905549.1|DC905549
EST:     TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACG                         CACACATTCCTCTTTATCNCTATCCATTTCTGAACACAGTAAGCAANACAA
genomic: TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACGgtatgcgtgg ... ttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
EST: gi|18369560|gb|BJ201648.1|BJ201648
EST:     TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACG                         CACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCA
genomic: TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACGgtatgcgtgg ... ttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCA
EST: gi|100356823|gb|BY965298.1|BY965298
EST:     TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACG                         CACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
genomic: TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACGgtatgcgtgg ... ttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
EST: gi|100368244|gb|BY948190.1|BY948190
EST:     TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACG                         CACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA
genomic: TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACGgtatgcgtgg ... ttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAA

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: 29 (upstream exon), 19 (downstream exon)
Score: 2

TGTGTAGCCTCACATCCGGACACTCGTGCTCTTTTCCTCAACGgtatgcgtgg ... ttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAAGACCGTTCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttaaagattcgggatgcagtttctgatcgtgtggttttatctttggttgcagCACACATTCCTCTTTATCTCTATCCATTTCTGAACACAGTAAGCAAGACAAGACCGTTCGAGTATCTTCGACTTACGAGCCTAGGAGTCATTGGTGCTCT
                       ttctgat  putative branch site (score: 2)
                                     ttttatcttt  putative PPT
                                     ttttatcttt  TA-rich tract