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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgactctgcaaagcattgaagcggcgttaggagtttggcgctattgcgtcggatgtgcatcctacattgagtttctagcgatggatcggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCACTCCGACCAGTTGTGCATTCTCAGACCTTGAAGTACAATTCTAAGATCCG

Basic information

species Physcomitrella patens
transcript PP1S126_52V6.1
intron # 2
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|162265032|gb|FC440911.1|FC440911
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162218145|gb|FC394982.1|FC394982
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162222749|gb|FC399003.1|FC399003
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67699691|gb|BJ959924.1|BJ959924
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67576194|gb|BJ949018.1|BJ949018
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67576216|gb|BJ949040.1|BJ949040
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67699716|gb|BJ959949.1|BJ959949
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162252357|gb|FC426165.1|FC426165
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162274823|gb|FC450850.1|FC450850
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67574166|gb|BJ946990.1|BJ946990
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162270108|gb|FC446184.1|FC446184
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67698454|gb|BJ958687.1|BJ958687
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67696535|gb|BJ956768.1|BJ956768
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|18351988|gb|BJ184040.1|BJ184040
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67697564|gb|BJ957797.1|BJ957797
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162243609|gb|FC421808.1|FC421808
EST:     TGTGAGGACCTGGGTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162252356|gb|FC426164.1|FC426164
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67573151|gb|BJ945975.1|BJ945975
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162274992|gb|FC450851.1|FC450851
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67576924|gb|BJ949748.1|BJ949748
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67572987|gb|BJ945811.1|BJ945811
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67696367|gb|BJ956600.1|BJ956600
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|67575015|gb|BJ947839.1|BJ947839
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
EST: gi|162218146|gb|FC394983.1|FC394983
EST:     TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGG                         CGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC
genomic: TGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCAC

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: 33 (upstream exon), 31 (downstream exon)
Score: 28

CATAACAATGTTATCCCCAATGGCCACTTCAAGAAGGACTGGCAAAACTATGTGAGGACCTGGTTTAACCAGCCCGCCCGCAAGAAAAGAAGAAGAACGGgttagcatcc ... ggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCACTCCGACCAGTTGTGCATTCTCAGACCTTGAAGTACAATTCTAAGATCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgactctgcaaagcattgaagcggcgttaggagtttggcgctattgcgtcggatgtgcatcctacattgagtttctagcgatggatcggttttgcagCGCGTCAAAAGAAGGCCGTGGCTGTGTTCCCACGCCCTACTGCTGGACCACTCCGACCAGTTGTGCATTCTCAGACCTTGAAGTACAATTCTAAGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - ctgcaaa