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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaacttgtttctaagcccgatcgtattcgtttacgttttcttgaattctcatatcgcattgaagctcacattggtgaatatttttctgttctgttcctttctttctatggattgagtggtcccttctgattatgcgtggttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG

Basic information

species Physcomitrella patens
transcript PP1S8_288V6.1
intron # 29
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|162189371|gb|FC366529.1|FC366529
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162259197|gb|FC435217.1|FC435217
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162153113|gb|FC329519.1|FC329519
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162189370|gb|FC366528.1|FC366528
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162155067|gb|FC330861.1|FC330861
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAN
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|100367439|gb|BY984706.1|BY984706
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162153021|gb|FC330051.1|FC330051
EST:     GAAACCAGTGGGAAGAAC                         TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: GAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162245992|gb|FC421881.1|FC421881
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162186821|gb|FC363065.1|FC363065
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         TGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162272382|gb|FC449034.1|FC449034
EST:     ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAAC                         GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: ACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
EST: gi|162256676|gb|FC433194.1|FC433194
EST:     GAAACCAG-TGGAAAGAAC                         GGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
genomic: GAAACCAGTTGG-AAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG

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: 52

TGTTATGGGTCAATTTGATCATGGACACTTTGGGAGCACTTGCACTTGCTACTGAGCCACCTACAGATGATCTTATGGATCGGAAACCAGTTGGAAGAACgtgaggaact ... gttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttctttctatggattgagtggtcccttctgattatgcgtggttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG
                              ttctgat  putative branch site (score: 52)
        tttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggaacttgtttctaagcccgatcgtattcgtttacgttttcttgaattctcatatcgcattgaagctcacattggtgaatatttttctgttctgttcctttctttctatggattgagtggtcccttctgattatgcgtggttcgtgcagGGAGCCATTGATCTCCAACATTATGTGGAGAAATATATTTGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA