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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgttttgcttgccgattgtatttttgttgcggtttgaaggttcatgcatcatcactttctggattccgttctcattcatgtgcatcgtatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGACACTTTGGGGGCTAGCTCTGCCGCTTTGTTCCAACGTACAGTATTCTTC

Basic information

species Physcomitrella patens
transcript PP1S207_106V6.1
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|37825514|gb|BJ583580.1|BJ583580
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|162255089|gb|FC430704.1|FC430704
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|18339849|gb|BJ171876.1|BJ171876
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|162201876|gb|FC377810.1|FC377810
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|162161546|gb|FC338753.1|FC338753
EST:     TTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: TTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|67692680|gb|BJ952913.1|BJ952913
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|208363515|gb|DC939734.1|DC939734
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|37828153|gb|BJ586165.1|BJ586165
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATNGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|162201875|gb|FC377809.1|FC377809
EST:     GCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATGGGAGTCATGGGTGATTTGGCTGA
genomic: GCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|67699176|gb|BJ959409.1|BJ959409
EST:     GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
genomic: GCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA
EST: gi|37824051|gb|BJ582117.1|BJ582117
EST:     ATTTATTCAGAATGTGTATCATGACAAAGACAG                         GGACGAAGTGGTAACTAAGGCTGCTATNGGAGTCATGGGTGATTTGGCTGA
genomic: ATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGA

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: 34 (upstream exon), 28 (downstream exon)
Score: 13

GTATTTTCCAAGGATTTAAATCTAACAAGGCGGAGCTGATGGCACCATACGCTGGACATATTCTGCAATTTATTCAGAATGTGTATCATGACAAAGACAGgtatggataa ... tatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGACACTTTGGGGGCTAGCTCTGCCGCTTTGTTCCAACGTACAGTATTCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcatcatcactttctggattccgttctcattcatgtgcatcgtatatctcagGGACGAAGTGGTAACTAAGGCTGCTATTGGAGTCATGGGTGATTTGGCTGACACTTTGGGGGCTAGCTCTGCCGCTTTGTTCCAACGTACAGTATTCTTC
                                             tatatct  TA-rich tract