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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggatttcaaaatatgctttgtgctgttgttaaactttgttaaccttacacagttaaattgtttcacatctagtaagggctgccacttgcgaattgttttggtccgacacatataaaccttctccaattctcaggactgttccgtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGGAATCTCGGCTTATGAGCGACAGCATCTCCAAAACGAGTAAAAGCATGTA

Basic information

species Physcomitrella patens
transcript PP1S9_234V6.1
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|162183943|gb|FC360249.1|FC360249
EST:     ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG                         GGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
genomic: ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
EST: gi|37823355|gb|BJ581421.1|BJ581421
EST:     ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG                         GGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
genomic: ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
EST: gi|18341786|gb|BJ173821.1|BJ173821
EST:     ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG                         GGCCCGGAGACTTGGTCCACTCACCGTCTCNTGAGGCAAGGTCACCAAGGG
genomic: ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
EST: gi|37831005|gb|BJ589017.1|BJ589017
EST:     GACAAGTCAGNTCGTTCTCCAG                         GGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
genomic: GACAAGTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
EST: gi|162255475|gb|FC431889.1|FC431889
EST:     ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG                         GGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
genomic: ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
EST: gi|37828323|gb|BJ586335.1|BJ586335
EST:     ATGTATCGGACTGTGAAAACTTCCGACAAGGTCAGGTCGTTCTCCAG                         GGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
genomic: ATGTATCGGACTGTGAAAACTTCCGACAA-GTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
EST: gi|18336785|gb|BJ168808.1|BJ168808
EST:     ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAG                         GGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG
genomic: ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGG

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), 31 (downstream exon)
Score: 13

ATGTATCGGACTGTGAAAACTTCCGACAAGTCAGGTCGTTCTCCAGgttggatttc ... gtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGGAATCTCGGCTTATGAGCGACAGCATCTCCAAAACGAGTAAAAGCATGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtccgacacatataaaccttctccaattctcaggactgttccgtttctgcagGGCCCGGAGACTTGGTCCACTCACCGTCTCCTGAGGCAAGGTCACCAAGGGAATCTCGGCTTATGAGCGACAGCATCTCCAAAACGAGTAAAAGCATGTA
                                         ttccgtttct  CT-rich tract
          acatataaa  TA-rich tract