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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctatgtcttcatctatgaacgtcataacaagttcgtgaaatgcgtaccttctgtatgatcctattgagttgagtttgatggtccctcgcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGAATTTTCCTACGGAAGTGATTTGTATAGAGATGAAGAAGACAGGCATAAT

Basic information

species Physcomitrella patens
transcript PP1S46_276V6.1
intron # 1
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|162187430|gb|FC362652.1|FC362652
EST:     GGATCCAAAATGCCTTTGAAAAAGCG                         ATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
genomic: GGATCCAAAATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
EST: gi|100412885|gb|BY992484.1|BY992484
EST:     GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCG                         ATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
genomic: GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
EST: gi|100411815|gb|BY992355.1|BY992355
EST:     GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCG                         ATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
genomic: GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
EST: gi|162235294|gb|FC412261.1|FC412261
EST:     AATGCCTTTGAAAAAGCG                         ATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
genomic: AATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
EST: gi|100431028|gb|BY959991.1|BY959991
EST:     GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCG                         ATTCGAGAAAGATGGAGGATGACG-TGCAAGAGATGATGGATATAATAG
genomic: GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAG-ATGACGGTGCAAGAGATGATGGATATAATAG
EST: gi|100446733|gb|CJ971032.1|CJ971032
EST:     GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCG                         ATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
genomic: GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
EST: gi|100420344|gb|BY975987.1|BY975987
EST:     GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCG                         ATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA
genomic: GGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGA

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: 31 (upstream exon), 24 (downstream exon)
Score: 5

CGAGTCCTGATAACGATGATGAAGATGACGAGGAATTCGACGACAGAGGGGGTCGCTCTGGCAAGCAGGCGAAAGGATCCAAAATGCCTTTGAAAAAGCGgtacaaattc ... gcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGAATTTTCCTACGGAAGTGATTTGTATAGAGATGAAGAAGACAGGCATAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtaccttctgtatgatcctattgagttgagtttgatggtccctcgcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGAATTTTCCTACGGAAGTGATTTGTATAGAGATGAAGAAGACAGGCATAAT
                              gtttgat  putative branch site (score: 5)
                                       tccctcgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctatgtcttcatctatgaacgtcataacaagttcgtgaaatgcgtaccttctgtatgatcctattgagttgagtttgatggtccctcgcgtttgcagATTCGAGAAAGATGGAGATGACGGTGCAAGAGATGATGGATATAATAGTGAATTTTCCTACGGAAGTGATTTGTATAGAGATGAAGAAGACAGGCATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG