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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaagctccacggccaattaccataaatatttcaagtttttttcgttacagtcacggtgataaattgctctcgcttgacgtggttgagcaggtaacaagagacatttttgtgctacggtatttaagtccactctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG

Basic information

species Physcomitrella patens
transcript PP1S54_186V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_186V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 4
gttaaagctccacggccaattaccataaatatttcaagtttttttcgttacagtcacggtgataaattgct-ctcgcttgacgtggttgagcaggtaaca-agagacatttttgtgctacggtatttaagtccactctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG
                                                         | |||     |||| ||  |||  | ||     ||  ||  || |   |||  |   ||||    |  || |   ||   | |||  ||| ||       ||||||||| ||  |    |||||||||||  |||| || || ||||| || || || |||||||||||||||||  ||||||| ||||| ||||||||||||
---------------------------------------------------------gttgaccttctgcttctttcttcgcatgcgcttgcctgttccataccaacacatcattgct----tgcttca---catctttattatattatcc------tcagGAAGGGTTTGCTGCTTTGTGGACTGGCATTGGACCCAATGTTGCGCGCAATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG

upper sequence: PP1S54_186V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G000510_T02 (Zea mays), 3'ss of exon 4
gttaaagctccacggccaattaccataaatatttcaagtttttttcgttacagtcacggtgataaattgctctcgcttgacgtggttgagcaggtaacaagagacatttttgtgctacggtatttaagtccactctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG
                                     || | |   |  |   ||    |   |  |  |   || | |   |  |||    | || |||   | |   ||       ||   |||       | |||| |  ||  ||  |  || |||||||  |  |     |||||||||| ||||| ||||| || || || || ||||||||||||||||| ||  ||||||||||||| ||||||||||||
-------------------------------------gtctgtgctggcatgctcttc-tcccagctaac---cgttcgctttctttgttttgctaccaatcaataaaattagagcttggctcttattatatgtgtgatgtgcttggctcatcctt-agGAAGGGGTTGCCGCTCTGTGGACTGGCCTTGGACCAAATGTAGCGCGGAATGCTATCATCAATGCTGCTGAGTTGGCCAGTTATGATCAAGTCAAGCAG

upper sequence: PP1S54_186V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv08s0007g01700.t01 (Vitis vinifera), 3'ss of exon 4
gttaaagctccacggccaattaccataaatatttcaagtttttttcgttacagtcacggtgataaattgctctcgcttgacgtggttgagcaggtaacaagagacatttttgtgcta-cggtatttaagtccactctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG
                                |  ||  | ||  | ||| |  ||   |  | | | | |      | |  |  || ||              ||||| | || |  |  |||  || |  |||   ||||   | |||   |||| |||| ||  |   |    |||||||||||||||| || || || ||  | || ||||| || |||||||| ||||| ||||||||||| ||||| ||||||
-------------------------------gtggaacatcttgcccttatatgcatattatttattagtttctttataatttatttaagttt-----------catttgtttgatgtctttatccaattttact--aatttg--tatctaaaattt-agGAGGGAGTTGGAGCTCTGTGGACTGGGCTTGGACCGAATGTAGCGAGAAATGCTATTATAAATGCTGCTGAACTAGCCAGTTATGATCAAGTGAAGCAG

upper sequence: PP1S54_186V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ24273 (Selaginella moellendorffii), 3'ss of exon 4
gttaaagctccacggccaattaccataaatatttcaagtttttttcgttacagtcacggtgataaattgctctcgcttgacgtggttgagcaggtaacaagagacatttttgtgctacggtatttaagtcc-actctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG
                                                                                                         ||        ||| || |||   ||| |    |   || |  |||  ||   |||||||||||| ||||| | |||||||| || |||||||| || || ||||||||||||||||| || ||||| || || || ||||| ||||| || |||
-------------------------------------------------------------------------------------------------------gtatggcgaacatactgtcttttcatcccaagtcggactcttcatctcata---cagGAAGGTTTCGCAAAACTTTGGACTGGCCTGGGTCCAAATGTGGCCCGTAACGCTATCATCAACGCGGCCGAGCTCGCTAGCTATGATCAAGTAAAACAG

upper sequence: PP1S54_186V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ35536 (Selaginella moellendorffii), 3'ss of exon 4
gttaaagctccacggccaattaccataaatatttcaagtttttttcgttacagtcacggtgataaattgctctcgcttgacgtggttgagcaggtaacaagagacatttttgtgctacggtatttaagtcc--actctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG
                                                                                                         ||        ||| || |||   ||   | || || | | |  |||  ||   |||||||||||| ||||| | |||||||| || |||||||| || || ||||||||||||||||| || ||||| || || || ||||| ||||| || |||
-------------------------------------------------------------------------------------------------------gtatggcgaacatactgtcttttcatctcaagtccgact-cttcatctcata---cagGAAGGTTTCGCAAAACTTTGGACTGGCCTGGGTCCAAATGTGGCCCGTAACGCTATCATCAACGCGGCCGAGCTCGCTAGCTATGATCAAGTAAAACAG

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|208374000|gb|DC944733.1|DC944733
EST:     CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAG                         GAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
genomic: CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAGgttaaagctc ... ggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
EST: gi|208372592|gb|DC944599.1|DC944599
EST:     TACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAG                         GAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
genomic: TACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAGgttaaagctc ... ggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
EST: gi|162230432|gb|FC407087.1|FC407087
EST:     CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAG                         GAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
genomic: CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAGgttaaagctc ... ggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
EST: gi|100428683|gb|BY959381.1|BY959381
EST:     CCCGCCGCTACAGCGGCGCTTTGAATGCTTATTCGACTATTGTCAAGCAG                         GAAGGTTTCCCAAAATTGGGGACTG
genomic: CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAGgttaaagctc ... ggtatttcagGAAGGTTTCACAAAATTGTGGACTG
EST: gi|162158108|gb|FC333903.1|FC333903
EST:     CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAG                         GAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
genomic: CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAGgttaaagctc ... ggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
EST: gi|162272364|gb|FC449029.1|FC449029
EST:     CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAG                         GAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC
genomic: CCCGCCGCTACAGCGGCGCTATGAATGCTTATTCGACTATTGTCAAGCAGgttaaagctc ... ggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttgtgctacggtatttaagtccactctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG
                            ctctgat  putative branch site (score: 4)
                                       ttttctg  putative PPT
                                 atttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaagctccacggccaattaccataaatatttcaagtttttttcgttacagtcacggtgataaattgctctcgcttgacgtggttgagcaggtaacaagagacatttttgtgctacggtatttaagtccactctgatttcattttctggtatttcagGAAGGTTTCACAAAATTGTGGACTGGGCTTGGTCCAAACGTTGCTCGTAACGCTATCATCAATGCTGCCGAACTGGCCAGTTATGACCAAGTCAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC