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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattagtctcaaaatgcactgagacttccgactccctataatttgaagttttcacgttcttgaggtcggatggttagcatactaatttcctctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATACAGAGGCACATGCACATGCACATGATCATAGTCACAGTCACGACCATGAC

Basic information

species Physcomitrella patens
transcript PP1S31_130V6.1
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|162156786|gb|FC333598.1|FC333598
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162197127|gb|FC372479.1|FC372479
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162157523|gb|FC333781.1|FC333781
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162242561|gb|FC419216.1|FC419216
EST:     TGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGCCCATGAGCATAC
genomic: TGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162253296|gb|FC428890.1|FC428890
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|208374619|gb|DC948619.1|DC948619
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|208351971|gb|DC925780.1|DC925780
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162184555|gb|FC360029.1|FC360029
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162151813|gb|FC328059.1|FC328059
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|18338140|gb|BJ170164.1|BJ170164
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|67725452|gb|BJ975711.1|BJ975711
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162184554|gb|FC360028.1|FC360028
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162195572|gb|FC371873.1|FC371873
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|37831922|gb|BJ589934.1|BJ589934
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162162261|gb|FC338043.1|FC338043
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162161773|gb|FC338213.1|FC338213
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162178673|gb|FC354462.1|FC354462
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162155636|gb|FC331561.1|FC331561
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162176070|gb|FC351864.1|FC351864
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|208373025|gb|DC948790.1|DC948790
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162187276|gb|FC363226.1|FC363226
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162155637|gb|FC331562.1|FC331562
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|37827407|gb|BJ585419.1|BJ585419
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162162411|gb|FC339168.1|FC339168
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162162262|gb|FC338044.1|FC338044
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162178674|gb|FC354463.1|FC354463
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|208356256|gb|DC946262.1|DC946262
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162157524|gb|FC333782.1|FC333782
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|208364862|gb|DC943680.1|DC943680
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162269789|gb|FC445657.1|FC445657
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
EST: gi|162269788|gb|FC445656.1|FC445656
EST:     GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAG                         AGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC
genomic: GAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATAC

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: 32 (upstream exon), 25 (downstream exon)
Score: 8

CGCATCAATGGGCTAGCTCAAGTGCGCAAGGCGAAGAAGGCTGAGGTGGACCTGGATTATGTCCTAGGTGTAGGTGGCTTTGATCTTGAAAGgttcgtgcat ... tctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATACAGAGGCACATGCACATGCACATGATCATAGTCACAGTCACGACCATGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttttcacgttcttgaggtcggatggttagcatactaatttcctctattgcagAGTTGAAGACGATATCTTGAAAGGCGTGAAGACCCCGGACCATGAGCATACAGAGGCACATGCACATGCACATGATCATAGTCACAGTCACGACCATGAC
                                  tactaat  putative branch site (score: 8)
                                        tttcctctatt  CT-rich tract
                                 atactaattt  TA-rich tract