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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATGAAGAATGCAACCAAAGTGTCTGTGGTTCTACCCACCGGAGAGGAACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctctttgccatttcggactattgccatggaagtatgacattgatacgcctctaggctatctctattcaacaacatccaccagcacaacttgataagtgcaccgtgtcaattttgtcgatctgcag

Basic information

species Physcomitrella patens
transcript PP1S49_263V6.1
intron # 3
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|162194064|gb|FC370239.1|FC370239
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|208383152|gb|DC907182.1|DC907182
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTANGGAGTGTGTACAAGAGGTTGTCTTTCGTANACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|18371387|gb|BJ202989.1|BJ202989
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|162203955|gb|FC380247.1|FC380247
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|100443698|gb|BY963795.1|BY963795
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|18364516|gb|BJ196589.1|BJ196589
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|67709326|gb|BJ965142.1|BJ965142
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCCGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|67712572|gb|BJ966021.1|BJ966021
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|18371459|gb|BJ203061.1|BJ203061
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGA
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGA
EST: gi|162193014|gb|FC371958.1|FC371958
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|162170538|gb|FC347671.1|FC347671
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|162182905|gb|FC359795.1|FC359795
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|162151107|gb|FC327639.1|FC327639
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|18365107|gb|BJ197181.1|BJ197181
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGAC
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGAC
EST: gi|67716577|gb|BJ966837.1|BJ966837
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|18368549|gb|BJ200634.1|BJ200634
EST:     CTCATTTGTGAATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTANGGAGTGTGTACA
genomic: CTCATTTGTGA-TTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACA
EST: gi|162237663|gb|FC413694.1|FC413694
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
EST: gi|162268191|gb|FC443869.1|FC443869
EST:     ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAA                         ATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG
genomic: ACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCG

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: 20 (upstream exon), 34 (downstream exon)
Score: 9

GCTATGAAGAATGCAACCAAAGTGTCTGTGGTTCTACCCACCGGAGAGGAACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctct ... cgatctgcagATGTAGGGAGTGTGTACAAGAGGTTGTCTTTCGTAGACCGGTACTTGTTCGTGTGGATCCTCGCCGTTATGGCAATCGCCCTCGTGGTGGGTTACAAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATGAAGAATGCAACCAAAGTGTCTGTGGTTCTACCCACCGGAGAGGAACTCATTTGTGATTCTGTTCTACCTTCCAAGCCTGGAGCTGACGTCCCAAgtaagcctctttgccatttcggactattgccatggaagtatgacattgatacgcctctaggctatctctattcaacaacatccaccagcacaacttgataagtgcaccgtgtcaattttgtcgatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA