Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgtcattttcaggtattacaccacaagaaatgtttctatgtttggtgcagttggatgtgtcctgattacatcaaatttgtttcaatttacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGGACTCCAGTGATGATGAGTTGAGCGAGGAAGAAGACTGCATGTCCAGCGA

Basic information

species Physcomitrella patens
transcript PP1S37_166V6.1
intron # 5
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|22492750|gb|BU052673.1|BU052673
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCA
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCA
EST: gi|67696838|gb|BJ957071.1|BJ957071
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162201846|gb|FC377780.1|FC377780
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|37832038|gb|BJ590050.1|BJ590050
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|67696647|gb|BJ956880.1|BJ956880
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162268532|gb|FC444405.1|FC444405
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162261485|gb|FC438321.1|FC438321
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162260434|gb|FC436087.1|FC436087
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162274058|gb|FC450130.1|FC450130
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|208353497|gb|DC922509.1|DC922509
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|208374764|gb|DC948694.1|DC948694
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|208396037|gb|DC915797.1|DC915797
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|37851038|gb|BJ609046.1|BJ609046
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162201845|gb|FC377779.1|FC377779
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162274057|gb|FC450129.1|FC450129
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162222561|gb|FC398712.1|FC398712
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|208361846|gb|DC950118.1|DC950118
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|37832758|gb|BJ590770.1|BJ590770
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|208378275|gb|DC918896.1|DC918896
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162222560|gb|FC398711.1|FC398711
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGANAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|37851815|gb|BJ609823.1|BJ609823
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162261484|gb|FC438320.1|FC438320
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
EST: gi|162268531|gb|FC444404.1|FC444404
EST:     CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAG                         AATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG
genomic: CGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGG

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: 41

CCTCAGCTCTTACTTTACCCTAATCCTACCGATCCTCTGAACGGTGAAGCCGCTGCGTTGATGATGCGAGACCGCGAGCACTATGAGCAGAAAGTGAAAGgtgcgtgtat ... tacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGGACTCCAGTGATGATGAGTTGAGCGAGGAAGAAGACTGCATGTCCAGCGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgcagttggatgtgtcctgattacatcaaatttgtttcaatttacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGGACTCCAGTGATGATGAGTTGAGCGAGGAAGAAGACTGCATGTCCAGCGA
                 tcctgat  putative branch site (score: 41)
                              aaatttgtttcaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgtcattttcaggtattacaccacaagaaatgtttctatgtttggtgcagttggatgtgtcctgattacatcaaatttgtttcaatttacgttgcagAATATTGTGAAAGATATGCAAAGGCAGAGGACATTGGAAGGCATCCAGAGGACTCCAGTGATGATGAGTTGAGCGAGGAAGAAGACTGCATGTCCAGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - -tggtgca