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

...gattttacgtaatcatagtatataaacagttaggagcatattggaatggaacaaatgtttatgttccagagggtaatgatgttgtgatttttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCTCTTGCTCCTCGAGATAATCATGAAGCTCAGGTGCAATTCGCTTTGGAGC

Basic information

species Physcomitrella patens
transcript PP1S43_170V6.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S43_170V6.4 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G31850.2 (Arabidopsis thaliana), 3'ss of exon 3
gattttacgtaatcatagtatataaacagttaggagcatattggaatggaacaaatgtttatgttccagagggtaatgatgttgtgatttttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCTCTTGCTCCTCGAGATAATCATGAAGCTCAGGTGCAATTCGCTTTGGAGC
               |||| | |   ||  ||      |  |  |||    ||  | |    | || ||    ||||  |   ||| ||| | ||   |||| || || |||||||| || ||| || |  | || ||  |  |  | |||||||||||  ||||||| |||||||||||||| ||||| ||| | || |
-------------gttagtctctcttcaactactcaagttctctaat----cagttctgatcggtcgaggttataatttt-ccgtggtttct-ttggtagGTTGCGAGCTGGGGAGGCGATCTTTTGGACCGTGGGATACTATCACTCTCTCTTGCTCCAAGAGATAACCATGAAGCTCAGGTTCAATTTGCTCTTGAAC
















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|162164338|gb|FC341516.1|FC341516
EST:     CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGG                         GTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
genomic: CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGGgtgagttctc ... ttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
EST: gi|162171558|gb|FC347499.1|FC347499
EST:     CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGG                         GTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
genomic: CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGGgtgagttctc ... ttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
EST: gi|162226907|gb|FC403095.1|FC403095
EST:     CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGG                         GTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
genomic: CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGGgtgagttctc ... ttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
EST: gi|162169959|gb|FC345899.1|FC345899
EST:     CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGG                         GTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
genomic: CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGGgtgagttctc ... ttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
EST: gi|208364567|gb|DC935352.1|DC935352
EST:     CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGG                         GTAGCCAGTTTGGGGAAGGGAAGCTTCTGAATAGGGGCATCNTGACNATGT
genomic: CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGGgtgagttctc ... ttatttccagGTAGCCAGTT-GGGGAGGGGA-GCTTCTGAATAGGGGCATCTTGACCATGT
EST: gi|162156233|gb|FC332049.1|FC332049
EST:     CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGG                         GTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
genomic: CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGGgtgagttctc ... ttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
EST: gi|100407198|gb|BY974050.1|BY974050
EST:     CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGG                         GTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT
genomic: CAGGAATGAAGGATGGCTCTGTTCGAACTGCCTTGGACACTGGTTGTGGGgtgagttctc ... ttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggaacaaatgtttatgttccagagggtaatgatgttgtgatttttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCTCTTGCTCCTCGAGATAATCATGAAGCTCAGGTGCAATTCGCTTTGGAGC
                                          tttttatttcc  CT-rich tract
                                    ttgtgatttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattttacgtaatcatagtatataaacagttaggagcatattggaatggaacaaatgtttatgttccagagggtaatgatgttgtgatttttatttccagGTAGCCAGTTGGGGAGGGGAGCTTCTGAATAGGGGCATCTTGACCATGTCTCTTGCTCCTCGAGATAATCATGAAGCTCAGGTGCAATTCGCTTTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG