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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctcacttttcttgaactgcacactctgtttggatttaagttctttacgtaatagcgtccatcttctgtataacctgtgtttgcaatgatagactgaaggatttcttaattttgaatcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAGGAGACCATGATTGGTTGCATTATTGGAACAGGGACAAACGCATGCTATG

Basic information

species Physcomitrella patens
transcript PP1S150_124V6.1
intron # 4
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|100445076|gb|BY964375.1|BY964375
EST:     TATGATCTCAGCCCTG                         GTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
genomic: TATGATCTCAGCCCTGgtatatctca ... tcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
EST: gi|162154067|gb|FC330302.1|FC330302
EST:     TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTG                         GTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
genomic: TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTGgtatatctca ... tcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
EST: gi|162186018|gb|FC361846.1|FC361846
EST:     TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTG                         GTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
genomic: TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTGgtatatctca ... tcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
EST: gi|100390444|gb|BY952852.1|BY952852
EST:     TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTG                         GTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
genomic: TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTGgtatatctca ... tcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
EST: gi|162165557|gb|FC340668.1|FC340668
EST:     TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTG                         GTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
genomic: TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTGgtatatctca ... tcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
EST: gi|162248551|gb|FC425327.1|FC425327
EST:     TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTG                         GTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG
genomic: TTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTGgtatatctca ... tcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAG

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: 4

GTGGGCAAAGACATCGTGAAGCAATTTCAGGATGCAATCAGCAGAAGTAACCATCAGATTATGATCTCAGCCCTGgtatatctca ... tcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAGGAGACCATGATTGGTTGCATTATTGGAACAGGGACAAACGCATGCTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctgtgtttgcaatgatagactgaaggatttcttaattttgaatcttttacagGTAAACGACACCGTTGGCACGTTGGCCGGAGGCAGATTCAACTTCGACGAGGAGACCATGATTGGTTGCATTATTGGAACAGGGACAAACGCATGCTATG
                                tcttaat  putative branch site (score: 4)
                                             tcttttac  putative PPT
                             atttcttaattttgaa  TA-rich tract