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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAACGAGCCCGCAAGTGCTACTAAGGACGGGTCCCTCCATGGCTACGAATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctcttacacttacactgctttcgtctcgtaatcgggctctgaattgtacatgctcatggggatctcgctttgtggggtgccggttccaacgttaa...

Basic information

species Physcomitrella patens
transcript PP1S96_83V6.1
intron # 1
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|100374839|gb|BY949090.1|BY949090
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|162261405|gb|FC438241.1|FC438241
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|208350212|gb|DC901596.1|DC901596
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|18328766|gb|BJ160771.1|BJ160771
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|100428382|gb|BY977777.1|BY977777
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|100452539|gb|CJ975321.1|CJ975321
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|162215832|gb|FC390897.1|FC390897
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|100356725|gb|BY965249.1|BY965249
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|100383086|gb|BY987007.1|BY987007
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|208400597|gb|DC904573.1|DC904573
EST:     AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTC-CTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
EST: gi|208371482|gb|DC931833.1|DC931833
EST:     AATCGCTCCATCGCTTGTTGTCTTCGGAGCTTCCACCGCATCTCTTCCAA                         GAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT
genomic: AATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCT

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: 21 (upstream exon), 32 (downstream exon)
Score: 7

GGAGAACGAGCCCGCAAGTGCTACTAAGGACGGGTCCCTCCATGGCTACGAATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctctt ... tttatggcagGAGGTGAGTCGCGTATTGTACGGGTGCAACAGAGGTAGTGCTGTCACTCCTGTCCCACAGACGGAGGACCTTAGTGCTGCAGCGAAGGAAGGGAATTTCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAACGAGCCCGCAAGTGCTACTAAGGACGGGTCCCTCCATGGCTACGAATCGCTCCATCGCTTGTTGTCCTCGGAGCTTCCACCGCATCTCTTCCAAgtgagctcttacacttacactgctttcgtctcgtaatcgggctctgaattgtacatgctcatggggatctcgctttgtggggtgccggttccaacgttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT