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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctcactcacgtttctcacctcctacacttcccgatctgcaatcctcttatctatccgcaatttgagctgaactcgagctgattttggtttttcgcgaacatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGAATTGTAGTAGTATACAAGAACGCGGTTATCAAGCACGGAACTGTAATCT

Basic information

species Physcomitrella patens
transcript PP1S98_52V6.1
intron # 5
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|37848144|gb|BJ606152.1|BJ606152
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|162165592|gb|FC341431.1|FC341431
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37851681|gb|BJ609689.1|BJ609689
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|18336430|gb|BJ168452.1|BJ168452
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|18341113|gb|BJ173146.1|BJ173146
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|162257014|gb|FC432753.1|FC432753
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|18336605|gb|BJ168628.1|BJ168628
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37834296|gb|BJ592308.1|BJ592308
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|162257013|gb|FC432752.1|FC432752
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37838689|gb|BJ596697.1|BJ596697
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACNGAC                         AATGTCTGGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37839942|gb|BJ597950.1|BJ597950
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|208382362|gb|DC919350.1|DC919350
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37851872|gb|BJ609880.1|BJ609880
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37848949|gb|BJ606957.1|BJ606957
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|162164570|gb|FC341865.1|FC341865
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|162165593|gb|FC341432.1|FC341432
EST:     GGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGANC                         A-TGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATC
genomic: GGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGA-Cgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATC
EST: gi|162248094|gb|FC420099.1|FC420099
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37838430|gb|BJ596438.1|BJ596438
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|18339910|gb|BJ171938.1|BJ171938
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|37852585|gb|BJ610593.1|BJ610593
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
EST: gi|67570080|gb|BJ942904.1|BJ942904
EST:     TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGAC                         AATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA
genomic: TGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGA

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: 35 (upstream exon), 35 (downstream exon)
Score: 259

AAAGGTACCTTTGGGCGTCGGCGAGAACTCAAAGCTGAGGAATTGTATTGTGGACAAGAATGCAAGAATTGGCAAGGATGTTGTCATTGCGAACACTGACgtaagtgctc ... acatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGAATTGTAGTAGTATACAAGAACGCGGTTATCAAGCACGGAACTGTAATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccgcaatttgagctgaactcgagctgattttggtttttcgcgaacatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGAATTGTAGTAGTATACAAGAACGCGGTTATCAAGCACGGAACTGTAATCT
                       agctgat  putative branch site (score: 259)
      aatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgctcactcacgtttctcacctcctacacttcccgatctgcaatcctcttatctatccgcaatttgagctgaactcgagctgattttggtttttcgcgaacatgcgcagAATGTCTTGGAAGCGGAGAGACAAAGTGAAGGTTTTTACATCCGTTCCGGAATTGTAGTAGTATACAAGAACGCGGTTATCAAGCACGGAACTGTAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC