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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaagtaatgtataaaagaagtatctgaaatggacatgctagcgtgttgtctagagctttatgagctgatgcaaatgatggtgatgctgaatggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.1
intron # 7
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|162169757|gb|FC345294.1|FC345294
EST:     ACGTCTCACTTTTGAAGTAC-TTGCT-CGNNATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ACGTCTCACTTTTGAAGTACTTTGCTCCG--ATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|18327390|gb|BJ159392.1|BJ159392
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|67727192|gb|BJ977451.1|BJ977451
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|67726751|gb|BJ977010.1|BJ977010
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|67718262|gb|BJ968521.1|BJ968521
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGANAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|162176349|gb|FC353534.1|FC353534
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGA
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGA
EST: gi|162181163|gb|FC357608.1|FC357608
EST:     GCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: GCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|37824766|gb|BJ582832.1|BJ582832
EST:     TTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCAC-TTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: TTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|67727852|gb|BJ978111.1|BJ978111
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|162223700|gb|FC399772.1|FC399772
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|19789330|gb|BQ041244.1|BQ041244
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|162169758|gb|FC345295.1|FC345295
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCAC
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCAC
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|18333553|gb|BJ165568.1|BJ165568
EST:     GCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: GCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|67720690|gb|BJ970949.1|BJ970949
EST:     TGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTNGGCGTCTGAGAAGATTATCCCTG
genomic: TGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|208375034|gb|DC944815.1|DC944815
EST:     GAAGTAC-TTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: GAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|67720235|gb|BJ970494.1|BJ970494
EST:     TGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: TGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
EST: gi|100403476|gb|BY991219.1|BY991219
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAAACCAG                         GTGGGTCTGCACTTTCTCTTACTTACTTGGCGTCTGA
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGA
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAG                         GTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG
genomic: ATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTG

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: 19 (upstream exon), 30 (downstream exon)
Score: 4

CTTATGGAGACCTCGCGCAAAGGTTACTTAGCTGCTGTCTCAGCCTCTACATACTCCTACGTCTCACTTTTGAAGTACTTTGCTCCGATCATGAACCCAGgtacggaacg ... atggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtctagagctttatgagctgatgcaaatgatggtgatgctgaatggattcagGTGGTTCTGCACTTTCTCTTACTTACTTGGCGTCTGAGAAGATTATCCCTGG
                  agctgat  putative branch site (score: 4)
            tttatga  TA-rich tract