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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAATGCGAAAGCCAAATTTACGGAGACCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatatcgagcttgcatctcctttggagcacagaatcttagttttgatgataaaatcaattatccttttctcaaagacgagggatagcttgaagta...

Basic information

species Physcomitrella patens
transcript PP1S94_163V6.1
intron # 2
splice site 5'
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|208377790|gb|DC940902.1|DC940902
EST:     CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAG                         ATGGNTCGTGGGGCCGCAACTCTTCCAAATGGAA
genomic: CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatat ... agaaatgcagATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAA
EST: gi|208365036|gb|DC931114.1|DC931114
EST:     CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAG                         ATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
genomic: CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatat ... agaaatgcagATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
EST: gi|208372432|gb|DC952276.1|DC952276
EST:     CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAG                         ATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
genomic: CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatat ... agaaatgcagATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
EST: gi|208369602|gb|DC936350.1|DC936350
EST:     CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAG                         ATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
genomic: CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatat ... agaaatgcagATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
EST: gi|67577911|gb|BJ950078.1|BJ950078
EST:     CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAG                         ATGGTTCGTGGGGCCGCAACTCTTCCAA-TGGAAGTGGCAAG
genomic: CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatat ... agaaatgcagATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
EST: gi|208362199|gb|DC939623.1|DC939623
EST:     CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAG                         ATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG
genomic: CCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatat ... agaaatgcagATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG

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: 26 (upstream exon), 18 (downstream exon)
Score: 2

GAGAATGCGAAAGCCAAATTTACGGAGACCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatat ... agaaatgcagATGGTTCGTGGGGCCGCAACTCTTCCAAATGGAAGTGGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAATGCGAAAGCCAAATTTACGGAGACCGTTGAAGCTCATGTTCGATTAGGGATAGATCCTAAAAGAAGTGACCAGgtatttatatcgagcttgcatctcctttggagcacagaatcttagttttgatgataaaatcaattatccttttctcaaagacgagggatagcttgaagta

- - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT