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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatgtgtttatctaggacagttggtcctgctgtcaatatattgaagaggtccagatcttgattttctttccatgtctgcttaaagatcgaatcgggtgcttacttgctcaagaaaaaatcctgagtaggaatctcttttctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCAAAGTTGTATGCCTGGTCAGGTAACCTGAGCACTGCCGAAAGCCAGAGGG

Basic information

species Physcomitrella patens
transcript PP1S100_30V6.1
intron # 15
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|162161220|gb|FC337283.1|FC337283
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|162256364|gb|FC432374.1|FC432374
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|100393142|gb|BY989764.1|BY989764
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCG
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|162185667|gb|FC362054.1|FC362054
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|162180210|gb|FC355527.1|FC355527
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|162228276|gb|FC404056.1|FC404056
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|162222679|gb|FC397491.1|FC397491
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|162255247|gb|FC431557.1|FC431557
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
EST: gi|162199756|gb|FC375829.1|FC375829
EST:     GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCG                         GTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA
genomic: GGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCA

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: 13 (upstream exon), 29 (downstream exon)
Score: 3

GAACATACCCACCCAGGTCACAAAGAACATTCAATAATGTTGGTGCGGGTGCGAGCTGCTGGTCCACACATTGTTGTAGCTGTACAACTAGAGCCGgtaaggatgt ... ctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCAAAGTTGTATGCCTGGTCAGGTAACCTGAGCACTGCCGAAAGCCAGAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgcttacttgctcaagaaaaaatcctgagtaggaatctcttttctgtttgcagGTTTCAGCTTCACTCAACTCCTCTGATTGCTTTCTGCTTCAAACCAGCTCAAAGTTGTATGCCTGGTCAGGTAACCTGAGCACTGCCGAAAGCCAGAGGG
  tgcttac  putative branch site (score: 3)
                                     tctcttttctgtttgc  putative PPT
               aagaaaaaat  TA-rich tract