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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagagaaacttctcattcaagttctttggtactttatccgcttgttgcagttaaacctagggtgtggttattttaccaatgtgccgtatgagagcatggtttgggtatgatggcaagtcttgttgtcagcatctgaagcgttcctgagtggggactgactgaccaatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTCTTCTCATGTTCTGGCCGAGCAACGAAG

Basic information

species Physcomitrella patens
transcript PP1S11_305V6.1
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|208350888|gb|DC909935.1|DC909935
EST:     TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAG                         GGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
genomic: TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
EST: gi|18345221|gb|BJ177262.1|BJ177262
EST:     TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAG                         GGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
genomic: TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
EST: gi|18367520|gb|BJ199603.1|BJ199603
EST:     TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAG                         GGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
genomic: TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
EST: gi|162226063|gb|FC401029.1|FC401029
EST:     TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAG                         GGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
genomic: TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
EST: gi|100403883|gb|BY955149.1|BY955149
EST:     TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAG                         GGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
genomic: TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
EST: gi|18355804|gb|BJ187863.1|BJ187863
EST:     TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAG                         GGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
genomic: TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
EST: gi|100393437|gb|BY953399.1|BY953399
EST:     TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAG                         GGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC
genomic: TCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTC

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: 33 (upstream exon), 29 (downstream exon)
Score: 10

GTGTAAGTGCTCATGAGAGGGTATCCTTAAGGTACACGCAATGGCGCACCTCTCTATCGAACGTTGTGGGGTGCCGAGCGGTTATGTCAGCTGAGAACAGgtgagagaga ... caatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTCTTCTCATGTTCTGGCCGAGCAACGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttgtcagcatctgaagcgttcctgagtggggactgactgaccaatcagcagGGACGTCTCGCCTACATCCTCTGAATTGAAGCAGAATGAAGGGGAGCCCTCTTCTCATGTTCTGGCCGAGCAACGAAG
                                      gactgac  putative branch site (score: 10)