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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgttccgtttttatctcagttactaaggattcaatgttattcggcattacgctggttttgtatctactattttaacagatgattgtcatatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGAAATCATGGCTCTAGCGAATGGTTCTCTGATTGTAGCACGACGGACCGAA

Basic information

species Physcomitrella patens
transcript PP1S76_162V6.1
intron # 1
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|208367273|gb|DC939831.1|DC939831
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACGTTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|100445252|gb|BY982881.1|BY982881
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|18372205|gb|BJ203807.1|BJ203807
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|18365810|gb|BJ197888.1|BJ197888
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|100429999|gb|BY978196.1|BY978196
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|208360547|gb|DC930847.1|DC930847
EST:     GGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: GGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|100451064|gb|CJ974579.1|CJ974579
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|18367612|gb|BJ199695.1|BJ199695
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|100428777|gb|BY959428.1|BY959428
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGN                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
EST: gi|208364204|gb|DC943432.1|DC943432
EST:     CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGT                         NNNNNNNTTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA
genomic: CAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGA

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: 24 (upstream exon), 12 (downstream exon)
Score: 1

GTCAACATTGGCAGATCCAGTGCAATCGCCTGTAACTTAGAAATTGAACACAGATCTACTTCAGGATCGGTTTCAAGTGCCCACCGACTCCTGTGGAAGTgtaagcatat ... atatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGAAATCATGGCTCTAGCGAATGGTTCTCTGATTGTAGCACGACGGACCGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcattacgctggttttgtatctactattttaacagatgattgtcatatgtgcagAAAAAAATTCACGTTTTCATTGACATTTGCGCTGCACATCCTTCAGGCAGAAATCATGGCTCTAGCGAATGGTTCTCTGATTGTAGCACGACGGACCGAA
                           ttttaac  putative branch site (score: 1)
                  tatctactattttaa  TA-rich tract