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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGGCTAGGGGAGATGCTGTCATATATCTCCGATTCCCACACTTCGGATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcatcatctgctgctatgattttatctagagatctcacgtttagtgttctttgattgtctgtgtcgacgtgttgatggcattcacgtcatggcatgagatcatggcttatgcgaggttttaccgaaatcgcag

Basic information

species Physcomitrella patens
transcript PP1S83_223V6.3
intron # 7
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|162195485|gb|FC369342.1|FC369342
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|162266758|gb|FC442274.1|FC442274
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|37821284|gb|BJ579350.1|BJ579350
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|208392973|gb|DC945995.1|DC945995
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGCGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|162152132|gb|FC328722.1|FC328722
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATGGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGATTTTTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|18337776|gb|BJ169800.1|BJ169800
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|162232988|gb|FC407875.1|FC407875
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|162278960|gb|FC454699.1|FC454699
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGATTTTTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|208394076|gb|DC957157.1|DC957157
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|37837828|gb|BJ595836.1|BJ595836
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|208371461|gb|DC955797.1|DC955797
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|162151616|gb|FC327745.1|FC327745
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|208365825|gb|DC951060.1|DC951060
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|67692840|gb|BJ953073.1|BJ953073
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|162278961|gb|FC454700.1|FC454700
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
EST: gi|162198268|gb|FC372607.1|FC372607
EST:     ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAG                         AAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA
genomic: ATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCA

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), 30 (downstream exon)
Score: 12

GCCATGGCTAGGGGAGATGCTGTCATATATCTCCGATTCCCACACTTCGGATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcat ... gaaatcgcagAAGCTGGAGGAGAAGTGTTTGATGCAGCAGGTGAGCCATTGGACTTCTCCAGAGGTAGATGGCTTGATTTGGATACCGGTATTATTGCCACCAATAAGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATGGCTAGGGGAGATGCTGTCATATATCTCCGATTCCCACACTTCGGATACCGTGAGAAAATTTGGGACCACGCCGCCGGAGCAATCGTCATAACAGgtatgatcatcatctgctgctatgattttatctagagatctcacgtttagtgttctttgattgtctgtgtcgacgtgttgatggcattcacgtcatggcatgagatcatggcttatgcgaggttttaccgaaatcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA