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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgggcttttccccaccttgtgacaacgtttatttgtgtcaaaaataacgtgaaatcatgtttcattggatcccaaccgatcgtcgtcgaggaacagcatcgctaagacggtatgttaagagattgaggttgttgaagtattggcgggtatgtggtgagtgagtgagtgtgtgtgttggatccggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCAAAATCTTCGATTCAATCACGGCAGAGAAGCTCAGCTTTAATGTGGAGTT

Basic information

species Physcomitrella patens
transcript PP1S419_7V6.1
intron # 1
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|18368530|gb|BJ200615.1|BJ200615
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
EST: gi|18355424|gb|BJ187483.1|BJ187483
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACG
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACG
EST: gi|18370120|gb|BJ201722.1|BJ201722
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTC
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGG-AGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTC
EST: gi|18362378|gb|BJ194448.1|BJ194448
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAG
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAG
EST: gi|18345560|gb|BJ177603.1|BJ177603
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAAGTGAAGAGGTGA
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGA-GTGAAGAGGTGA
EST: gi|18325654|gb|BJ157651.1|BJ157651
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAGTGA
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGA
EST: gi|18328493|gb|BJ160498.1|BJ160498
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAGTGAAGAGGT
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGT
EST: gi|100358118|gb|BY965481.1|BY965481
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
EST: gi|18328995|gb|BJ161001.1|BJ161001
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
EST: gi|18354843|gb|BJ186902.1|BJ186902
EST:     AGGGGAAAGAAAGTGACTTTCCAGCTTGTGGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAGTGAAGAG
genomic: AGGGGAAAGAAAGTGACTTTCCAGCTTGTG-AGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAG
EST: gi|100388094|gb|BY988567.1|BY988567
EST:     AGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTNCA-                         GCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCCTC-AGGGCTGGCT
genomic: AGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACT-CAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCC-TCCAGGGCTGGCT
EST: gi|18371544|gb|BJ203146.1|BJ203146
EST:     CATGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGANGTCGACTCAA                         GCACAGGGGAGCTTGTGACG
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACG
EST: gi|18345914|gb|BJ177957.1|BJ177957
EST:     GGGGGAAAGAAAGTGACTTTCCAGCTTGTGGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAG
genomic: GGGG-AAAGAAAGTGACTTTCCAGCTTGTG-AGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAG
EST: gi|67569679|gb|BJ942503.1|BJ942503
EST:     CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
genomic: CAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCA
EST: gi|18357135|gb|BJ189194.1|BJ189194
EST:     AGGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAA                         GCACAGGGGAGCTTGTGACGAG
genomic: AGGGG-AAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAG

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), 32 (downstream exon)
Score: 57

TTCGACGTGATGGATCGCGTTGCGGACATCCAGGACGACGCCAGTGAGCTCAGGGGAAAGAAAGTGACTTTCCAGCTTGTGAGCAGCGAGGTCGACTCAAgtgagttggg ... ggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCAAAATCTTCGATTCAATCACGGCAGAGAAGCTCAGCTTTAATGTGGAGTT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgggcttttccccaccttgtgacaacgtttatttgtgtcaaaaataacgtgaaatcatgtttcattggatcccaaccgatcgtcgtcgaggaacagcatcgctaagacggtatgttaagagattgaggttgttgaagtattggcgggtatgtggtgagtgagtgagtgtgtgtgttggatccggaatggcagGCACAGGGGAGCTTGTGACGAGTGAAGAGGTGACCCTCCAGGGCTGGCTCAAAATCTTCGATTCAATCACGGCAGAGAAGCTCAGCTTTAATGTGGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG