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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttgaatccttcaagtgttgtgcaagaagtggcatcactcaccgtctggtgagttctctgtccatgtttccaaactgaaacttcgtgttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGGAGGTTCGGCTTGGTCTGTCAAAGGGCCCCGTTTCACGCATGTTCTTTTA

Basic information

species Physcomitrella patens
transcript PP1S9_363V6.1
intron # 4
splice site 3'
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|67693691|gb|BJ953924.1|BJ953924
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|19776828|gb|BQ039121.1|BQ039121
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|67579124|gb|BJ951275.1|BJ951275
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|18347726|gb|BJ179773.1|BJ179773
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAAGCATG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAA-GCATG
EST: gi|7583863|gb|AW699766.1|AW699766
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|162220259|gb|FC395679.1|FC395679
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTCCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|67576775|gb|BJ949599.1|BJ949599
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|67718482|gb|BJ968741.1|BJ968741
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|18325360|gb|BJ157356.1|BJ157356
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|67507848|gb|BJ940724.1|BJ940724
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|18339020|gb|BJ171046.1|BJ171046
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|67700310|gb|BJ960543.1|BJ960543
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|18333307|gb|BJ165321.1|BJ165321
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|37826798|gb|BJ584810.1|BJ584810
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|67570416|gb|BJ943240.1|BJ943240
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|18325443|gb|BJ157439.1|BJ157439
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|18333399|gb|BJ165413.1|BJ165413
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
EST: gi|67726932|gb|BJ977191.1|BJ977191
EST:     GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATG                         ATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG
genomic: GTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGG

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), 34 (downstream exon)
Score: 13

ATTCCAGCGCCCAACTGGCCTTATTCCTTCATCCATGCTTGGTCTTGAGTCATTGACTGGAGAATTAGACGAATTTGGATTTGAAGACTTCTTGAATGgcaagttctt ... ttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGGAGGTTCGGCTTGGTCTGTCAAAGGGCCCCGTTTCACGCATGTTCTTTTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttgaatccttcaagtgttgtgcaagaagtggcatcactcaccgtctggtgagttctctgtccatgtttccaaactgaaacttcgtgttgtgttcagATCCGAAGGAGTCGGATACGTTCGTTCCTCAGGATATGCATGAAAGCATGGAGGTTCGGCTTGGTCTGTCAAAGGGCCCCGTTTCACGCATGTTCTTTTA

- tgttgaa