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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattgatcttcttttgctttttcgaattaggttttcgcatttgcaatgtcacatgttgtggagtaagcacgaaattggggagatgaatgacatggtagagttgtgacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGGGCATGAATGCGTGGTTGTTCGTGCACACCGAGGAGATTCCTGGGGCACT

Basic information

species Physcomitrella patens
transcript PP1S76_199V6.1
intron # 1
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|162212957|gb|FC389173.1|FC389173
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|19789383|gb|BQ041278.1|BQ041278
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|162210326|gb|FC386772.1|FC386772
EST:     TTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: TTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|100445348|gb|BY982977.1|BY982977
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|18368954|gb|BJ201039.1|BJ201039
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|162238278|gb|FC417315.1|FC417315
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|162210327|gb|FC386773.1|FC386773
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|162216711|gb|FC393583.1|FC393583
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|162238279|gb|FC417316.1|FC417316
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|67578136|gb|BJ950303.1|BJ950303
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|162215598|gb|FC391365.1|FC391365
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
EST: gi|100378824|gb|BY968707.1|BY968707
EST:     GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTG                         GCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG
genomic: GGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGG

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: 26 (upstream exon), 27 (downstream exon)
Score: 4

GGAATCAAGTACACCGGGTTGACTGTGAAGCAGATGCAGCAGCTGCGAAAGGCGTTGCCGCAGGAAACCACTCTCATGGTGGCCAAGAACAAGCTGATTGgtaatattga ... gacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGGGCATGAATGCGTGGTTGTTCGTGCACACCGAGGAGATTCCTGGGGCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagtaagcacgaaattggggagatgaatgacatggtagagttgtgacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGGGCATGAATGCGTGGTTGTTCGTGCACACCGAGGAGATTCCTGGGGCACT
            aaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattgatcttcttttgctttttcgaattaggttttcgcatttgcaatgtcacatgttgtggagtaagcacgaaattggggagatgaatgacatggtagagttgtgacttagcagGCAAGGCAATTGAGGGTACGGAATGGGAGGCTTTGAAACCCGCCCTTAAGGGCATGAATGCGTGGTTGTTCGTGCACACCGAGGAGATTCCTGGGGCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT