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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttcatagttactcttctgcatctctttgcaaattatatttaattcctggtgtatctttcaaagtgttactgctatcatgcctttctcaccaccttggccttattctatgggatcctgtgcgtactactgtcaagttgacctaaatggtttttcttttgttcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTTAAGTTTCTTGAGGTGGACGAGGAGCGTACACGCCTCGTTCTCAGCAACA

Basic information

species Physcomitrella patens
transcript PP1S40_14V6.1
intron # 3
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|19783627|gb|BQ040046.1|BQ040046
EST:     TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
genomic: TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
EST: gi|162279659|gb|FC455385.1|FC455385
EST:     TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACA
genomic: TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACA
EST: gi|162190540|gb|FC366178.1|FC366178
EST:     TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
genomic: TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
EST: gi|162186279|gb|FC361587.1|FC361587
EST:     TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
genomic: TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
EST: gi|162206261|gb|FC382331.1|FC382331
EST:     TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
genomic: TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
EST: gi|19790819|gb|BQ042072.1|BQ042072
EST:     TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
genomic: TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
EST: gi|100399261|gb|BY954281.1|BY954281
EST:     TAGCCGTTGAGGGTCTGCGTGGTTTCGTTTCCTTTTTCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACA
genomic: TAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACA
EST: gi|162205699|gb|FC381901.1|FC381901
EST:     CCTTTTCCCAGATTTCAGCT                         AGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT
genomic: CCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTT

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: 20

ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCTgtaagtgttt ... tcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTTAAGTTTCTTGAGGTGGACGAGGAGCGTACACGCCTCGTTCTCAGCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgcgtactactgtcaagttgacctaaatggtttttcttttgttcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTTAAGTTTCTTGAGGTGGACGAGGAGCGTACACGCCTCGTTCTCAGCAACA
                       acctaaa  putative branch site (score: 20)
                                 tttttcttttgttcct  putative PPT
                                 tttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttcatagttactcttctgcatctctttgcaaattatatttaattcctggtgtatctttcaaagtgttactgctatcatgcctttctcaccaccttggccttattctatgggatcctgtgcgtactactgtcaagttgacctaaatggtttttcttttgttcctttgcagAGGGGAGCCCAATCCAATCCTGAGGAACTACTGAACAAGGAGATTCCCCTTAAGTTTCTTGAGGTGGACGAGGAGCGTACACGCCTCGTTCTCAGCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG