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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgaagctctgcagtgttcgtatcttcttttttacgaaatgacttcatggttttcttttgtacaccacttacaagcacctctatctttatatttaggtcattctttcttatacataacgtcattatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA

Basic information

species Physcomitrella patens
transcript PP1S47_23V6.2
intron # 3
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|208382438|gb|DC927972.1|DC927972
EST:     CTCATTGGTTGAGTTCATGCTGAAAGAAANCAGAGACTCTGCATGCCAAA                         GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
genomic: CTCATTGGTTGAGTTCATGCTGAAAGAAA-CAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
EST: gi|100399470|gb|BY972735.1|BY972735
EST:     GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAA                         GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
genomic: GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
EST: gi|208398077|gb|DC904382.1|DC904382
EST:     GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAA                         GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
genomic: GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
EST: gi|100451193|gb|CJ974643.1|CJ974643
EST:     GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAA                         GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTT-CCTGAGGACTTA
genomic: GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
EST: gi|162223997|gb|FC400355.1|FC400355
EST:     GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAA                         GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
genomic: GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
EST: gi|100351812|gb|BY964562.1|BY964562
EST:     GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAA                         GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTTCCTGAGGACTT
genomic: GCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTT-CCTGAGGACTT
EST: gi|100409507|gb|BY955967.1|BY955967
EST:     CTCATTGGTTGAGTTCATGCTGAAAAGAAACAGAGACTCTGCATGCCAAA                         GTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA
genomic: CTCATTGGTTGAGTTCATGCTGAAA-GAAACAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTA

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: 21 (upstream exon), 24 (downstream exon)
Score: 4

CAACGCTCCTACATATGATGAAAATTCTTTCTCTATTCCAGGATTTAAAGGCTCATTGGTTGAGTTCATGCTGAAAGAAACAGAGACTCTGCATGCCAAAgtgagtttga ... tatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatctttatatttaggtcattctttcttatacataacgtcattatcgggcagGTGCGGAGGTATCAAGCGCCCGACGAACATCCTTTCTTTCCTGAGGACTTATCTCAACCTATTTTACCCAGCCTTCCAAAGTCCAGA
                                 acataac  putative branch site (score: 4)
                         tttcttatacataa  TA-rich tract