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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGTGAACGTCTACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcgttacatttctttcagacgcattttttttttaagtgtaattgttgataatttccatgcagcgaaattggaatcccttgtgagttcttagtg...

Basic information

species Physcomitrella patens
transcript PP1S269_30V6.2
intron # 11
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|208348107|gb|DC916917.1|DC916917
EST:     CAAAGTTGTGAGGGGAAGAGGTACCAG-TTTAGAACGGCGTTGGCAATG                         CTCNTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: CAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|67696733|gb|BJ956966.1|BJ956966
EST:     ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCTTGCCA-TTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208376570|gb|DC922601.1|DC922601
EST:     ACAAAGNTGTGA-GGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCNTGCCATTTTGGACTCNTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208381414|gb|DC927850.1|DC927850
EST:     ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208344725|gb|DC905174.1|DC905174
EST:     ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208394434|gb|DC928486.1|DC928486
EST:     ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208397506|gb|DC916390.1|DC916390
EST:     ACNAAGTTGTGAGGGGAAGAGGTACCAG-TTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208347298|gb|DC925322.1|DC925322
EST:     ACAAAGTT-TGA-GGGAAGAGGTACCAG-TTTAGAACNGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208356794|gb|DC926805.1|DC926805
EST:     ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208363842|gb|DC943299.1|DC943299
EST:     ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208380224|gb|DC919060.1|DC919060
EST:     ACNAAGTTGTGAGGGGAAGAGGTACCAG-TTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208355907|gb|DC926668.1|DC926668
EST:     ACAAAGNTGTGAGGGGAAGAGGTACCAG-TTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|100395052|gb|BY953582.1|BY953582
EST:     ACNAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: ACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
EST: gi|208354673|gb|DC918699.1|DC918699
EST:     GGGGAAGAGGTACCAGTTTTAGAACNGCGTNGGCAATG                         CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG
genomic: GGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG

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: 17 (upstream exon), 34 (downstream exon)
Score: 2

TTTTGTGAACGTCTACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcg ... tgttttgcagCTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGTGAACGTCTACAAAGTTGTGAGGGGAAGAGGTACCAGTTTTAGAACGGCGTTGGCAATGgtatccctcgttacatttctttcagacgcattttttttttaagtgtaattgttgataatttccatgcagcgaaattggaatcccttgtgagttcttagtg

- - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - AAGAGG