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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcactacaccttcgcatcccaaatcaatgtctgcactgtttgttcttctttagatcatctggcatgtcttatcacattcacgcatttgacaaccgcctaacactgtcctataatatggctttccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAAATGCCAGGACTCATCACTGACTTCCTCATTTCACTTGATGATCGATTCT

Basic information

species Physcomitrella patens
transcript PP1S11_387V6.1
intron # 6
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|162161906|gb|FC338281.1|FC338281
EST:     GCACAATGGTCCGNNNNNNNAAGAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GCACAATGGTCCGTTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|162174753|gb|FC352169.1|FC352169
EST:     GCACAATGGTCCGNNNNNNNAAGAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GCACAATGGTCCGTTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|162151131|gb|FC327650.1|FC327650
EST:     GAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|162212622|gb|FC389014.1|FC389014
EST:     AAGAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCNTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: AAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|162189384|gb|FC366542.1|FC366542
EST:     GCACAATGGTCCGNNNNNNNAAGAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GCACAATGGTCCGTTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|208353106|gb|DC921850.1|DC921850
EST:     GATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCATNCATNGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|208384431|gb|DC928182.1|DC928182
EST:     GCACAATGGTCCGNNNNNNNAAGAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GCACAATGGTCCGTTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|37845309|gb|BJ603317.1|BJ603317
EST:     GCACAATGGTCCGNNNNNNNAAGAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GCACAATGGTCCGTTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|208374862|gb|DC956135.1|DC956135
EST:     AAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: AAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|208359243|gb|DC954166.1|DC954166
EST:     CACAATGGTCCGNNNNNNNNAAGAAAGATGACGACACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: CACAATGGTCCG-TTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
EST: gi|208382645|gb|DC919813.1|DC919813
EST:     GCACAATGGTCCGNNNNNNNAAGAAAGATGACGGCACGTGGGATACGCAG                         GTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA
genomic: GCACAATGGTCCGTTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAA

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), 33 (downstream exon)
Score: 31

CTTGCATGATCCGAGCAAGGCAGTGGGATATGTGGGAGCTGCCTTGAGCAGCACAATGGTCCGTTTTTTTAAGAAAGATGACGACACGTGGGATACGCAGgtgattcact ... tccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAAATGCCAGGACTCATCACTGACTTCCTCATTTCACTTGATGATCGATTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacgcatttgacaaccgcctaacactgtcctataatatggctttccatgccagGTTGCCGTAACTGTGCCTGCATTGAAGGTGCGAAACTGGATATTGCCAGAAATGCCAGGACTCATCACTGACTTCCTCATTTCACTTGATGATCGATTCT
                  gcctaac  putative branch site (score: 31)
                                          ctttccat  putative PPT
                                tataatat  TA-rich tract