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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaggaacttgtgctagagctgagtgtatttggtggggtggtaggagggtgggtgaaggtgaaagtggggagggattgtttgcagtgcgtgaaggcacgggagggttttctgagtgtatgtgtgtgtgtgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATAAAGTACGAGACACGACCGAACCGGAAGGGATATAAGGCGGGGGCATTAC

Basic information

species Physcomitrella patens
transcript PP1S65_194V6.1
intron # 2
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|100414306|gb|BY992712.1|BY992712
EST:     ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGG                         GAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
genomic: ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
EST: gi|100448737|gb|CJ973036.1|CJ973036
EST:     ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCATACTACCAGG                         GAGCTGGTGCAAGTANAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
genomic: ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
EST: gi|100387749|gb|BY951749.1|BY951749
EST:     ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGG                         GAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGGGCAAGGGGATCAACATA
genomic: ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
EST: gi|100390843|gb|BY989326.1|BY989326
EST:     ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGG                         GAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
genomic: ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
EST: gi|100450218|gb|CJ974153.1|CJ974153
EST:     ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGG                         GAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
genomic: ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
EST: gi|100432630|gb|BY978670.1|BY978670
EST:     ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGG                         GAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
genomic: ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
EST: gi|100376967|gb|BY949553.1|BY949553
EST:     CGGATGATCATTTCA-GTGCTGGACGACTCGACGGATCAGACTACCCAGG                         -AGCTGGTGCAAGTAAGA-GTGCAGCGGTGGGCGA-CAAGGGGATC
genomic: CGGATGATCATT-CAAGTGCTGGACGACTCGACGGATCAGACTACC-AGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTA-GAAGTGCAGCGGTGGGCGAGCAAGGGGATC
EST: gi|100392974|gb|BY989700.1|BY989700
EST:     ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGG                         GAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA
genomic: ACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATA

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: 13

GTGTACCAACTGTCGATACAGGCGGCGTGCGGGCTGTCGTGGCCGCAGGACCGGATGATCATTCAAGTGCTGGACGACTCGACGGATCAGACTACCAGGgtagaggaac ... tgtggtccagGAGCTGGTGCAAGTAGAAGTGCAGCGGTGGGCGAGCAAGGGGATCAACATAAAGTACGAGACACGACCGAACCGGAAGGGATATAAGGCGGGGGCATTAC




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