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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtctgcaaaatttaatgcctttcgacattcctcttcaaagccactggtcataacctctttaaagattcataattcgaagtctgtttcttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAG

Basic information

species Physcomitrella patens
transcript PP1S73_243V6.1
intron # 6
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|162155914|gb|FC332463.1|FC332463
EST:     GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAG                         GTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC
genomic: GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC
EST: gi|162160113|gb|FC335983.1|FC335983
EST:     GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAG                         GTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC
genomic: GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC
EST: gi|100377934|gb|BY949596.1|BY949596
EST:     GCTTGGANNAGCTTCCAGAGATCATGGTTGGCGATGAAAGCATTGTGGAG                         GTGGCGAGACATCCAGAAGCCGTTACNNTGT-GT-ACANGAATTTGT-GGT
genomic: GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGAAGCCGTTAC--TGTTGTTACAGGAATT-GTTGGT
EST: gi|67569708|gb|BJ942532.1|BJ942532
EST:     GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAN                         GTGGCGAGACATCCAGA
genomic: GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGA
EST: gi|100449469|gb|CJ973768.1|CJ973768
EST:     GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAN                         GTGGCGAGACATCCAGAAGCCGTTACTG
genomic: GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTG
EST: gi|208344624|gb|DC912570.1|DC912570
EST:     GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAANGCATTGTGGAG                         GTGGCGAGACATCCANAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC
genomic: GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC
EST: gi|19780903|gb|BQ039624.1|BQ039624
EST:     GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAG                         GTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC
genomic: GCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGC

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: 32 (upstream exon), 34 (downstream exon)
Score: 5

GGCAGTCAAGGAGGCCTCATCAGTGCCTGCACTAAGAGAAGCTCTTGCTGGCTTGGAAAAGCTTCCAGAGATCATGGTTGGCGATGAAGGCATTGTGGAGgttagtcttt ... ttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggtcataacctctttaaagattcataattcgaagtctgtttcttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAG
     tcataac  putative branch site (score: 5)
                                     tctgtttcttcc  putative PPT
               tttaaagattcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtctgcaaaatttaatgcctttcgacattcctcttcaaagccactggtcataacctctttaaagattcataattcgaagtctgtttcttccgatcagGTGGCGAGACATCCAGAAGCCGTTACTGTTGTTACAGGAATTGTTGGTTGCGCAGGATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - -ctgcaaa