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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgctgacattttttcagggaggatgagctatttatattgaatgatttcgagcttaaaaattactcaacagtttcttgtttgtttcttttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG

Basic information

species Physcomitrella patens
transcript PP1S207_36V6.1
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|208390402|gb|DC933447.1|DC933447
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|100389837|gb|BY971189.1|BY971189
EST:     GGTTACAACAGTTTGGAAGTATT-ACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|100386396|gb|BY951192.1|BY951192
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|18356799|gb|BJ188858.1|BJ188858
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGT
EST: gi|162174230|gb|FC350613.1|FC350613
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|100381804|gb|BY950182.1|BY950182
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|208389011|gb|DC937344.1|DC937344
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|208390592|gb|DC937524.1|DC937524
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|100352556|gb|BY945331.1|BY945331
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|100353825|gb|BY983329.1|BY983329
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
EST: gi|208387516|gb|DC933379.1|DC933379
EST:     GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAG                         ATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT
genomic: GGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGAT

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: 28 (upstream exon), 31 (downstream exon)
Score: 7

GGTGATTTTGTGGATCGAGGTTACAACAGTTTGGAAGTATTTACAATACTTTTGCTGCTGAAAGCAAGgtacggtgag ... ttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttcgagcttaaaaattactcaacagtttcttgtttgtttcttttgtttgcagATACCCTGCTCATATGACGTTGTTGAGGGGTAACCATGAGAGTAGACAGATAACTCAG
                            tttcttgtttgtttct  CT-rich tract
          ttaaaaattactcaa  TA-rich tract