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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttgattttctggccgttggtattgttgtcttgcttagggttgattacatagataactttaagtgtacaacctgatcttatgtttactctgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGTAGACATTTCATGTCACAG

Basic information

species Physcomitrella patens
transcript PP1S83_77V6.1
intron # 5
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|100414390|gb|BY992752.1|BY992752
EST:     GCAAGCTGGAGACGGCTGTTCTGAAGAGATATCGAAGGCATTTTAAGCTG                         GTTGAAGTTGGTCCGAACTCATCANAAGAACAGCTTGTGGATGCAGTTTGT
genomic: GCAAGCTGGAGACGGCTGTTCTGAAGAGATATCGAAGGCATTTTAAGCTGgtaattattt ... tgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGT
EST: gi|67694900|gb|BJ955133.1|BJ955133
EST:     GAAGAGATATCGAAGGCATTTTAAGCTG                         GTTGAAG-TGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGT
genomic: GAAGAGATATCGAAGGCATTTTAAGCTGgtaattattt ... tgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGT
EST: gi|162174824|gb|FC352240.1|FC352240
EST:     GCAAGCTGGAGACGGCTGTTCTGAAGAGATATCGAAGGCATTTTAAGCTG                         GTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGT
genomic: GCAAGCTGGAGACGGCTGTTCTGAAGAGATATCGAAGGCATTTTAAGCTGgtaattattt ... tgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGT
EST: gi|162174823|gb|FC352239.1|FC352239
EST:     GCAAGCTGGAGACGGCTGTTCTGAAGAGATATCGAAGGCATTTTAAGCTG                         GTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGT
genomic: GCAAGCTGGAGACGGCTGTTCTGAAGAGATATCGAAGGCATTTTAAGCTGgtaattattt ... tgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGT

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), 34 (downstream exon)
Score: 4

TCTGTGAATCTTAGCAAGCTGGAGACGGCTGTTCTGAAGAGATATCGAAGGCATTTTAAGCTGgtaattattt ... tgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGTAGACATTTCATGTCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatagataactttaagtgtacaacctgatcttatgtttactctgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGTAGACATTTCATGTCACAG
                                      tttactct  CT-rich tract
        ataactttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttgattttctggccgttggtattgttgtcttgcttagggttgattacatagataactttaagtgtacaacctgatcttatgtttactctgttgtgaagGTTGAAGTTGGTCCGAACTCATCAAAAGAACAGCTTGTGGATGCAGTTTGTAGACATTTCATGTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC