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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAAGTTTCACAGAAGACCCGGGCTGCCCTGGCTGTTGCTGAAGAGAACGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattgattccatgatgtgtttttcagatctcaatttattgttatttgactgcttcttttggtgctcatttgatgaagtagcgatgtgcttcacat...

Basic information

species Physcomitrella patens
transcript PP1S9_32V6.1
intron # 5
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|37821240|gb|BJ579306.1|BJ579306
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208359056|gb|DC957804.1|DC957804
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208370262|gb|DC952084.1|DC952084
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208368298|gb|DC955509.1|DC955509
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208391878|gb|DC945957.1|DC945957
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|162265877|gb|FC442464.1|FC442464
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|162225889|gb|FC402181.1|FC402181
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|162280268|gb|FC456285.1|FC456285
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208361039|gb|DC957518.1|DC957518
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208368003|gb|DC951014.1|DC951014
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208347341|gb|DC925337.1|DC925337
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|162240162|gb|FC418289.1|FC418289
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|162280269|gb|FC456286.1|FC456286
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208353493|gb|DC922505.1|DC922505
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|162230914|gb|FC406753.1|FC406753
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208351287|gb|DC922066.1|DC922066
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208386854|gb|DC953507.1|DC953507
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
EST: gi|208371385|gb|DC955721.1|DC955721
EST:     CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAG                         GTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG
genomic: CGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAG

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: 22 (upstream exon), 34 (downstream exon)
Score: 5

TATCAAGTTTCACAGAAGACCCGGGCTGCCCTGGCTGTTGCTGAAGAGAACGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattg ... cttcctccagGTGCAAGTTGGGTTACAGGAGCGTTTTCAAGAGTCCAGAAGGTTGCTGCAGAGGTAAGTCAGAAGACCATCGAGAAGGCCCACACTATGGAAACTGATCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCAAGTTTCACAGAAGACCCGGGCTGCCCTGGCTGTTGCTGAAGAGAACGTTAAAACTGCAGGGTCTGCTCTCATGAAGAACCGATACATATTAACAGgtgtctattgattccatgatgtgtttttcagatctcaatttattgttatttgactgcttcttttggtgctcatttgatgaagtagcgatgtgcttcacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC