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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgctgatttgaaggtccttattagcactgtgcctatggctttgtagactatatcacggcgaatcatctaacgtgtccacctttgtgaaacatgggatgccgttgctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGA

Basic information

species Physcomitrella patens
transcript PP1S20_16V6.1
intron # 9
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|162166683|gb|FC342652.1|FC342652
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCCACCC
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCC-ACCC
EST: gi|67694426|gb|BJ954659.1|BJ954659
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|37851885|gb|BJ609893.1|BJ609893
EST:     TTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATNTGCTTCATGAGCCACCCA
genomic: TTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|208363930|gb|DC947202.1|DC947202
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|162196486|gb|FC375439.1|FC375439
EST:     GAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCC
genomic: GAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTC-AAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCC
EST: gi|161970273|gb|EE296246.1|EE296246
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|162180983|gb|FC358637.1|FC358637
EST:     GAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGGTGGTGCGTGCTATCTGCTTCATGAGCCACCC
genomic: GAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAA-GGTGGTGCGTGCTATCTGCTTCATGAGCCACCC
EST: gi|37827350|gb|BJ585362.1|BJ585362
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|37844517|gb|BJ602525.1|BJ602525
EST:     CAAGAAAGTNGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|162229880|gb|FC404333.1|FC404333
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|37836338|gb|BJ594346.1|BJ594346
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
EST: gi|18341638|gb|BJ173673.1|BJ173673
EST:     CCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAG                         GTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA
genomic: CCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCA

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: 16

AGAATTTGATGAAATGGGTCAAGTTATGGGGGTTACTTCCGAGGGGGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGATCCATCGTATTTGCCCAATAAGgtaatttgct ... gctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaatcatctaacgtgtccacctttgtgaaacatgggatgccgttgctttctcagGTCAAAAAGGTTGGGAAGGTGGTGCGTGCTATCTGCTTCATGAGCCACCCAATTCCAAATACCAATAATTCTGACTCCGTTCAAATCATTCTGCCACAGA
      atctaac  putative branch site (score: 16)
                                           ttgctttctc  putative PPT