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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtgtgattgaagtctttgttgagcaatgagtcttcatttggcattcgacaagctcttcctacgcttaaactgacctgtagaagttttctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG

Basic information

species Physcomitrella patens
transcript PP1S9_391V6.1
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|100363885|gb|BY966219.1|BY966219
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
EST: gi|100355079|gb|BY964990.1|BY964990
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
EST: gi|100441261|gb|BY962550.1|BY962550
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
EST: gi|100438381|gb|BY979928.1|BY979928
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
EST: gi|162267810|gb|FC443800.1|FC443800
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
EST: gi|162274567|gb|FC451010.1|FC451010
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
EST: gi|100389520|gb|BY988998.1|BY988998
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
EST: gi|100364726|gb|BY947877.1|BY947877
EST:     GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGG                         GTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
genomic: GGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG

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: 31 (upstream exon), 35 (downstream exon)
Score: 22

GATCCTGTCATTCGGAACCTGGATGAGTTGGATTCGAGAACCTTGCAAGGGCTCCTCGGCGAAATTCCTCTATGGGTGAAGAACCCAGATTACCATCGGgtaatggcac ... ctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgacaagctcttcctacgcttaaactgacctgtagaagttttctattttcagGTGGATTGGGTGAACAGGTTCTTAAAGGACATCTGGCCTTATCTTGATAAG
                         aactgac  putative branch site (score: 22)
                                         ttttctattttc  putative PPT
                                      aagttttctatttt  TA-rich tract