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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtttctcgtgcagatttggcaatgtgtcaaagatgtagcattagtgtcaatgcacgcagggtgtctcacatgtctttgcatgtttttctctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGAAGCTGCTGTGGAGGAGTACGCACAGAAGTACCCTGAGGAGGGTGCCGAG

Basic information

species Physcomitrella patens
transcript PP1S120_127V6.1
intron # 4
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|162230960|gb|FC407215.1|FC407215
EST:     AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|162219706|gb|FC395910.1|FC395910
EST:     AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|162176306|gb|FC352763.1|FC352763
EST:     AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|162166851|gb|FC343028.1|FC343028
EST:     GCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: GCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|162198697|gb|FC374817.1|FC374817
EST:     AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|162219889|gb|FC396704.1|FC396704
EST:     AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|100356519|gb|BY946406.1|BY946406
EST:     AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|100400286|gb|BY954401.1|BY954401
EST:     TATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: TATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
EST: gi|162209022|gb|FC385574.1|FC385574
EST:     AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAG                         CCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA
genomic: AACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGA

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: 34 (upstream exon), 35 (downstream exon)
Score: 41

CTGTGCACGGTGCAGCGTTGGGAGGCAAGGAGGTGGAGGCGACTCGGCAGAACCTGGGATGGCCATATGAGCCCTTCCACGTGCCCGACGAGGTCAAGAGgtgagtacaa ... tctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGAAGCTGCTGTGGAGGAGTACGCACAGAAGTACCCTGAGGAGGGTGCCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcaatgcacgcagggtgtctcacatgtctttgcatgtttttctctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGAAGCTGCTGTGGAGGAGTACGCACAGAAGTACCCTGAGGAGGGTGCCGAG
                   gtctcac  putative branch site (score: 41)
                                     tgtttttctct  putative PPT
                                    atgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtttctcgtgcagatttggcaatgtgtcaaagatgtagcattagtgtcaatgcacgcagggtgtctcacatgtctttgcatgtttttctctgtggcagCCACTGGAGCAAGCACACTGACCTGGGAACCAAGTACCAGAGCGAGTGGGAAGCTGCTGTGGAGGAGTACGCACAGAAGTACCCTGAGGAGGGTGCCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatgt