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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacatatatatatatatatatatatatatatatattcacacagggtacaacctccattacaagccatttacgtagtctcgctgtttttggtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCCAACGATTACGATAACTTCACAAAAAGAGCTTACGTAGGAAAGTGGAAAA

Basic information

species Physcomitrella patens
transcript PP1S196_120V6.1
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|162173385|gb|FC349556.1|FC349556
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162269611|gb|FC445570.1|FC445570
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|208351029|gb|DC925992.1|DC925992
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|208393495|gb|DC949657.1|DC949657
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|37853247|gb|BJ611255.1|BJ611255
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|37836056|gb|BJ594064.1|BJ594064
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|208362311|gb|DC954557.1|DC954557
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162194044|gb|FC370219.1|FC370219
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162161882|gb|FC338270.1|FC338270
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162244378|gb|FC423825.1|FC423825
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162220775|gb|FC395544.1|FC395544
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|208377352|gb|DC927040.1|DC927040
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162220776|gb|FC395545.1|FC395545
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|7066996|gb|AW496851.1|AW496851
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTTGA-GC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATT-GAAGC
EST: gi|162195675|gb|FC370338.1|FC370338
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|37845833|gb|BJ603841.1|BJ603841
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACANAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTNGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162194043|gb|FC370218.1|FC370218
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162175015|gb|FC351122.1|FC351122
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|162214018|gb|FC390425.1|FC390425
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|37841407|gb|BJ599415.1|BJ599415
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|208349342|gb|DC918050.1|DC918050
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
EST: gi|37844878|gb|BJ602886.1|BJ602886
EST:     TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCT                         GTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC
genomic: TGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCC

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: 25 (upstream exon), 25 (downstream exon)
Score: 10

ATGGAGGGCATTCATGAAAGACCAAATTAAAAGAGCTAGAGTGTTCTTTGTGGAGGCTGAGAAAGGTGTACGTGAGCTGGACAAAGACAGTCGCTGGCCTgtaagtaaaa ... gtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCCAACGATTACGATAACTTCACAAAAAGAGCTTACGTAGGAAAGTGGAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacaacctccattacaagccatttacgtagtctcgctgtttttggtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCCAACGATTACGATAACTTCACAAAAAGAGCTTACGTAGGAAAGTGGAAAA
           attacaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacatatatatatatatatatatatatatatatattcacacagggtacaacctccattacaagccatttacgtagtctcgctgtttttggtgtcaacagGTGTGGTCCGCCCTCATTCTTTACCAGCAAATTCTGGACGCCATTGAAGCCAACGATTACGATAACTTCACAAAAAGAGCTTACGTAGGAAAGTGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA