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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatttcctctggagttgtacagtctttttgcgaagtatttgcttctgtttatgcaaattggtgacgagcgtttgtggacatttgctgtgtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG

Basic information

species Physcomitrella patens
transcript PP1S61_202V6.1
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|162262550|gb|FC439541.1|FC439541
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
EST: gi|18347210|gb|BJ179256.1|BJ179256
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCGCTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
EST: gi|162275765|gb|FC451936.1|FC451936
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
EST: gi|162162081|gb|FC338872.1|FC338872
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
EST: gi|37826384|gb|BJ584396.1|BJ584396
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCGCTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
EST: gi|162262536|gb|FC439540.1|FC439540
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
EST: gi|162272506|gb|FC448508.1|FC448508
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
EST: gi|162272507|gb|FC448509.1|FC448509
EST:     TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCG                         ATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
genomic: TGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG

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: 18 (upstream exon), 34 (downstream exon)
Score: 7

CTTCGAACGGGGTGGTGATTGCCACAGAGAAGAAGCTCCCTTCAATTCTTGTCGATGAATCTTCGgtgagtcatc ... gtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttatgcaaattggtgacgagcgtttgtggacatttgctgtgtgttttcagATAAACAAGATTCAGTCACTGACGCCAAATATCGGAGTCGTCTACAG
                                              tgttttc  CT-rich tract
           aaatt  TA-rich tract