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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCCATGCAAAGCACGTTGAGAAGGAGTTAGTGGCCCTGGGATCCTCAACTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagctttaatcaatactacagcttcctttgctatcttgctagagaaatcttaaatctgaatcaaaagatctggaatggcactaattgtgatgttttctgttggcag

Basic information

species Physcomitrella patens
transcript PP1S158_40V6.1
intron # 28
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|7648281|gb|AW739264.1|AW739264
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|162155461|gb|FC330957.1|FC330957
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|162234653|gb|FC410399.1|FC410399
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|7648232|gb|AW739215.1|AW739215
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|162155462|gb|FC330958.1|FC330958
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|162178754|gb|FC354504.1|FC354504
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|67701389|gb|BJ961622.1|BJ961622
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|208347785|gb|DC917548.1|DC917548
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|67578489|gb|BJ950656.1|BJ950656
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|162186214|gb|FC362146.1|FC362146
EST:     CTGCAGCACTGAAGGCCCTCCCTCANGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
EST: gi|162197920|gb|FC373961.1|FC373961
EST:     CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCG                         GTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG
genomic: CTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTG

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: 18 (upstream exon), 18 (downstream exon)
Score: 1

GCTCCATGCAAAGCACGTTGAGAAGGAGTTAGTGGCCCTGGGATCCTCAACTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagcttta ... ctgttggcagGTGGATGCATCCACAAGATCCCAGTTGGTGGAGGAGCTCAAGCGGGCCCTGGATTCTTTGTCGAATTGACAAATGCCATTGTTTATACTTCTATCAGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCCATGCAAAGCACGTTGAGAAGGAGTTAGTGGCCCTGGGATCCTCAACTGCAGCACTGAAGGCCCTCCCTCAGGGTTTGGACGCACTGCTGCGCTCGgtaagctttaatcaatactacagcttcctttgctatcttgctagagaaatcttaaatctgaatcaaaagatctggaatggcactaattgtgatgttttctgttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC