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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcacccttcttggttcactggattttggggattcctttgcttaatgttcttcctttggtatcatgtcgaaattcctgctttgtttatttacttatttttgtctgcctatttttctttttcaacctttctaacattcactttcacgttaaactgattttgttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG

Basic information

species Physcomitrella patens
transcript PP1S97_78V6.2
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|67696433|gb|BJ956666.1|BJ956666
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67571063|gb|BJ943887.1|BJ943887
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67571535|gb|BJ944359.1|BJ944359
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|162260531|gb|FC435105.1|FC435105
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67572512|gb|BJ945336.1|BJ945336
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67696650|gb|BJ956883.1|BJ956883
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|162279259|gb|FC455806.1|FC455806
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|162278150|gb|FC454385.1|FC454385
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|18332577|gb|BJ164590.1|BJ164590
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67569399|gb|BJ942223.1|BJ942223
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|162279258|gb|FC455805.1|FC455805
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|162260530|gb|FC435104.1|FC435104
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67578333|gb|BJ950500.1|BJ950500
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67699663|gb|BJ959896.1|BJ959896
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67573050|gb|BJ945874.1|BJ945874
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|162246687|gb|FC425280.1|FC425280
EST:     GTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67571332|gb|BJ944156.1|BJ944156
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|162246688|gb|FC425281.1|FC425281
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67694652|gb|BJ954885.1|BJ954885
EST:     TCGTCATGGTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: TCGTCATGGTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67573265|gb|BJ946089.1|BJ946089
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67576166|gb|BJ948990.1|BJ948990
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67692660|gb|BJ952893.1|BJ952893
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67695885|gb|BJ956118.1|BJ956118
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67572806|gb|BJ945630.1|BJ945630
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67694374|gb|BJ954607.1|BJ954607
EST:     TTCGTCATGGTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: TTCGTCATGGTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67572841|gb|BJ945665.1|BJ945665
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67571783|gb|BJ944607.1|BJ944607
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|18329135|gb|BJ161141.1|BJ161141
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
EST: gi|67694876|gb|BJ955109.1|BJ955109
EST:     GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGG                         CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
genomic: GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG

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: 197

GTGAAGTACGCGAGGGACCCGGATAATTCGACCAAGGgtatggcacc ... gttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttcaacctttctaacattcactttcacgttaaactgattttgttatcacagCCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG
                                         ttttgtt  CT-rich tract
                                        attttgttat  TA-rich tract