Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGGTGGAATCTGCTTAAAGGAAGGGTAGATGAAATGGCAGAATGGGGTTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattccgtcgccacatcacggctatcatccgataaatctcttctattttctaaactttggcgatgtgtttatttttcatctgatacgctaaatttttcgacggatgatcaaaagaacggactggctaagactacacgttatttgttataaatcag

Basic information

species Physcomitrella patens
transcript PP1S7_147V6.1
intron # 8
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|100410694|gb|BY992222.1|BY992222
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
EST: gi|18345589|gb|BJ177632.1|BJ177632
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
EST: gi|18366459|gb|BJ198538.1|BJ198538
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTC
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTC
EST: gi|100449470|gb|CJ973769.1|CJ973769
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAA-GATG
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
EST: gi|100369228|gb|BY985073.1|BY985073
EST:     TTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCCTCAGG                         GTTAC-TACCTCGAGACTTGTATTCCCTTGA-TACGCCATATG
genomic: TTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCC-TCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCC-TTGAATACGCCATATG
EST: gi|100388161|gb|BY988634.1|BY988634
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
EST: gi|18342421|gb|BJ174456.1|BJ174456
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTTGAAT
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAAT
EST: gi|18343173|gb|BJ175211.1|BJ175211
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTT
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTT
EST: gi|100393532|gb|BY953438.1|BY953438
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
EST: gi|100394469|gb|BY972084.1|BY972084
EST:     TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAG                         GTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG
genomic: TTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATG

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: 31 (upstream exon), 29 (downstream exon)
Score: 5

CCTTGGTGGAATCTGCTTAAAGGAAGGGTAGATGAAATGGCAGAATGGGGTTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattcc ... tataaatcagGTTACCTACCTCGAGACTTGTATTCCTTGAATACGCCATATGGCAAAGATGGTGAGCTTCGGGATCTAGTACGTAAGATAAACGAGAGGGGTATACGAGC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTGGTGGAATCTGCTTAAAGGAAGGGTAGATGAAATGGCAGAATGGGGTTTCACGTCTTTGTGGCTACCTCCTCCCTGGGACTCTCTAGCTCCTCAAGgtctgattccgtcgccacatcacggctatcatccgataaatctcttctattttctaaactttggcgatgtgtttatttttcatctgatacgctaaatttttcgacggatgatcaaaagaacggactggctaagactacacgttatttgttataaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC