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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcagacctccacatattattgcctgttggttctttccatcatctgataatcgaaacgtgcctggatttatctgctgcatataattaactcttcgctcactttaattcttttaaatgatgaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAACCATTTTTAAGGGACAAATTAGTGATCAGGGTCAGAATTCTGGGCTTTGC

Basic information

species Physcomitrella patens
transcript PP1S98_233V6.1
intron # 5
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|67698313|gb|BJ958546.1|BJ958546
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|18339190|gb|BJ171217.1|BJ171217
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|162207047|gb|FC382161.1|FC382161
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|162208289|gb|FC384393.1|FC384393
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|162207048|gb|FC382162.1|FC382162
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|6227423|gb|AW156022.1|AW156022
EST:     AGGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: AGGTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|162238515|gb|FC417396.1|FC417396
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|67574887|gb|BJ947711.1|BJ947711
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|162208290|gb|FC384394.1|FC384394
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
EST: gi|162238514|gb|FC417395.1|FC417395
EST:     GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATT                         GACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC
genomic: GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAAC

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), 35 (downstream exon)
Score: 38

GTTTACTGGCTGCAATTTGGACAATACTTCGCAAGGAACGCTATTgtacgcagac ... gaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAACCATTTTTAAGGGACAAATTAGTGATCAGGGTCAGAATTCTGGGCTTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatataattaactcttcgctcactttaattcttttaaatgatgaattggcagGACCGAGACGATTTCGCGCTGGAGTTGGCCGTAGCCGACGAGTAGGGCAACCATTTTTAAGGGACAAATTAGTGATCAGGGTCAGAATTCTGGGCTTTGC
                          tttaattcttttaaat  TA-rich tract