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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcgatcaccgcccatttctatttgagaagtgttacttaggttggattgcagactgcacgattttggtgccccgatgttgtcagtttcttgtatgtagtgtttatttcaacgcttgcgtaactcgcttcatgtgcctgttgaccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCGCCATTTTATGACCCACTGGCTAATGTGGACGACGGATCCTGCCCATTCA

Basic information

species Physcomitrella patens
transcript PP1S99_42V6.3
intron # 7
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|162257183|gb|FC433059.1|FC433059
EST:     CTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTNCA-GAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTG
genomic: CTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATT-CAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTG
EST: gi|162257182|gb|FC433058.1|FC433058
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
EST: gi|162195533|gb|FC371834.1|FC371834
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
EST: gi|162226250|gb|FC402958.1|FC402958
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
EST: gi|162226251|gb|FC402959.1|FC402959
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
EST: gi|162207626|gb|FC384079.1|FC384079
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
EST: gi|162159900|gb|FC336153.1|FC336153
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
EST: gi|162227789|gb|FC402704.1|FC402704
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
EST: gi|162227790|gb|FC402705.1|FC402705
EST:     TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGG                         GGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG
genomic: TCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCG

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: 22

GGAGCTTGCACACGAAGGAGCGTGCGAAAATGCAATCTTTCCGGACTCTGTCTATGTTCAAGATCGCTGCGTTTTCCCAGCAGGAATGATTCAAGAAGGGgtattcgatc ... ccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCGCCATTTTATGACCCACTGGCTAATGTGGACGACGGATCCTGCCCATTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttatttcaacgcttgcgtaactcgcttcatgtgcctgttgaccttgttcagGGAGATCGGTGTGATTTGGATATTGTGCCTGGATGCACCGACCCGGAATCGCCATTTTATGACCCACTGGCTAATGTGGACGACGGATCCTGCCCATTCA
                                       tgttgac  putative branch site (score: 22)
                                             ccttgttc  CT-rich tract
     tatttcaa  TA-rich tract