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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttctcatatctctgaattggttgaaatggttttggttagatttattatatgtttgatttagttgaatgctgtctaatattttttgtgtgcaccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACTGAGTTGCTAGCAGATTTTCAGAAAGAGACTGCTGAGTACCGCTGAGGGA

Basic information

species Physcomitrella patens
transcript PP1S400_36V6.1
intron # 19
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|67695989|gb|BJ956222.1|BJ956222
EST:     GAAGAGGAAACANGCAAAAAACAA                         GNGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: GAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|37843737|gb|BJ601745.1|BJ601745
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|208362840|gb|DC950640.1|DC950640
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|162185105|gb|FC362239.1|FC362239
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|18341395|gb|BJ173430.1|BJ173430
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCGTGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|67692629|gb|BJ952862.1|BJ952862
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|162162677|gb|FC338979.1|FC338979
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|37836488|gb|BJ594496.1|BJ594496
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|37841576|gb|BJ599584.1|BJ599584
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
EST: gi|37849444|gb|BJ607452.1|BJ607452
EST:     AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAA                         GTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT
genomic: AATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACT

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), 31 (downstream exon)
Score: 7

ATCCGAGAAGCTCAGTTGGCGCAATTTAACTACATTCTTGTCGTTGGCGAAGAGGAAACAAGCAAAAAACAAgttggtttct ... caccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACTGAGTTGCTAGCAGATTTTCAGAAAGAGACTGCTGAGTACCGCTGAGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatatgtttgatttagttgaatgctgtctaatattttttgtgtgcaccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACTGAGTTGCTAGCAGATTTTCAGAAAGAGACTGCTGAGTACCGCTGAGGGA
                          gtctaat  putative branch site (score: 7)
                         tgtctaatatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtttctcatatctctgaattggttgaaatggttttggttagatttattatatgtttgatttagttgaatgctgtctaatattttttgtgtgcaccgtgtagGTGAACATCCGTACGCGAGATAATGTTGTGCATGGCACCAAGTCTGTTACTGAGTTGCTAGCAGATTTTCAGAAAGAGACTGCTGAGTACCGCTGAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA