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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgggattagtgatatgaagagaataacacacactcacatatatatatatatatatatatatatatatatataaatccatttgccgtgttccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGC

Basic information

species Physcomitrella patens
transcript PP1S83_44V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_44V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------------------------ttgggat-----tagtgatat-gaagagaataacacacactcacatatatatatatatatatata--tatatatatatataaatccatttg-------ccgtgttccttgtg-cagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGC
                                                                                |||||||     |  |||| | ||||   | |   | ||   ||  |||  |   | |   | |   ||  | ||  |||  | | || ||          | ||  || || ||| | || || ||||| ||| | |||||||| ||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||  |||| || ||||| |
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggttagatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
















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|208389513|gb|DC945779.1|DC945779
EST:     ACCCAGACA-TGTGTATGAAGAGGTCATCA-TGACAATTGCTGCATGATG                         TTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
genomic: ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttca ... ccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
EST: gi|162167332|gb|FC342320.1|FC342320
EST:     ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATG                         TTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
genomic: ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttca ... ccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
EST: gi|208371954|gb|DC951931.1|DC951931
EST:     ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATG                         TTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
genomic: ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttca ... ccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
EST: gi|162182877|gb|FC359780.1|FC359780
EST:     ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATG                         TTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
genomic: ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttca ... ccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
EST: gi|162160957|gb|FC336994.1|FC336994
EST:     ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATG                         TTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
genomic: ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttca ... ccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
EST: gi|67723757|gb|BJ974016.1|BJ974016
EST:     ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATT-CTGCATGATG                         TTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC
genomic: ACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttca ... ccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTAC

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: 21 (upstream exon), 15 (downstream exon)
Score: 1

TGTTGCAGGGAAATAGCTGCTGAGTACCCAGACATTGTGTATGAAGAGGTCATCATTGACAATTGCTGCATGATGgtaagtttca ... ccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatatatatatatatatatatataaatccatttgccgtgttccttgtgcagTTGGTAAAGAACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGC
                                         tgttcctt  CT-rich tract
     atatatatatatatat  TA-rich tract