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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA

Basic information

species Physcomitrella patens
transcript PP1S340_7V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                                         |    |    | | ||| |  | |  ||| |  |  | ||| | ||||    ||    | |      || | | |        ||| | |||| |     |  | |||   | ||||||| || || ||||||||| |||  || ||||| || ||||| ||| |||||||||||||||||||||| || ||||| ||| |||| ||||| ||| 
----------------------------------------gtaggtttc-cagaacctgtgatgtctaatcagctaat-gtttattcatccatttgcttttgtaatccacaagtca-----tgctttaactaatatgt---ggttctct---gtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                       | |  |     |  ||  ||   ||| ||     ||          |||| || || |       ||  | | |  || |  |||  |           |     |    | || |  |   |  |||   |||| ||||| || ||||||||| |||  ||||||||||||||||| |||||||| || || || || ||||| || || || ||| ||||||| || ||| 
-----------------------gtatgtctcctgaaatc-tgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 7
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                                          |  ||    ||   ||  || |   | ||  |   ||  |||||    |   | |    |    |||  ||  |  |  | | |||  ||      |||| | |    | | |||| ||||| |||||||||||| |||  ||||||||||||||||| || |||||||||||||| |||||||| |||||||| ||  | ||||| || ||| 
---------------------------------------gtcggtctcaacaa---cttatgctcaaattgctgaagtttgtcagtggctttcctcagtaggccatttatcac--aactaacgtgttctgta------ttggtcct----ctgtagATCCATTCAAGGAAAATGAATGTAAATCCTGATGTCAACTTTGAAGAATTGGCTCGCTCAACTGATGACTTCAACGGAGCACAGCTAAAGGCAGTTTGTG

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggctt-actacttagttttcattttcaataat-tttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                                               ||      |  ||| | | ||||    ||    ||  |||| |||| | | ||    |||| |||   ||| |    |    | | || |||  || |  |   || | |||| ||||| || ||||||||  |||  || ||||||||||| || || ||||||||||||||||||||||| |||||||| ||  ||||||| || ||| 
--------------------------------------------gtcggtctccacaacttatgttcaatttgctgaagttt--gtca-atgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 8
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                                           ||   |  |  |  ||| |    |     |   |   ||| ||  | ||  |  |  |      ||  ||| |      |  ||| | |||      |  || | |   | |||| || ||||||||||||||| | |  || |||||||||||||| |||||||| || ||||| ||||| || || || |||||  | |||||||| ||  
-------------------------------------------aataagaaagggattctagcccccctc--caatccccttcggttttgtggctcccaaa-----ctagcactaa------aggttccaaaataacgccgatctatgttgtgtagATCCACTCGAGGAAAATGAATGTGAATCCAGATGTCAACTTTGAAGAGTTGGCGCGTTCAACCGATGATTTCAATGGCGCTCAGCTAAAGGCTGTTTGCG

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 8
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                                                                           | ||| |   |  ||   || |  |   | |||  |  | |      |  || | | | |    |    ||  ||   ||||| ||||||||||| |||||| |    || |||||||||||||| ||  | ||||| || |||||||| || || ||||||||| |||||||||| ||| 
---------------------------------------------------------------------------gtttggtgtctt-taaacttcatctgctgacttgtttttcaaacagaacatttactgactgctctcactttgatatttcagATCCATTCGAGGAAGATGAATGTTCACCCAGATGTCAACTTTGAAGAACTTGCTCGGTCCACAGATGATTTCAATGGAGCTCAACTGAAGGCTGTTTGTG

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 8
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttact-acttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                                                                                                  ||     ||| ||    |||  |  ||||| |   |   |||     ||||    ||||||||| ||||||||||||| | | ||  | ||||| |||||||||||| |||| ||||| || || ||||| || || |||||| | ||||| |||||  
--------------------------------------------------------------------------------------------------gttcgttcttcctcgtctagactgtattttgatcgaaagtct-----tttcgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG

upper sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 8
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
                                                                                                         | | || | | || |  | | |   |   |     | | |||     ||||||||| ||||||||||||| | | ||  | ||||| |||||||||||| |||| ||||| || || ||||| || || |||||| | ||||| |||||  
------------------------------------------------------------------------------------------------------gttcgttcttcctcgtctagactgtattttgatcgaaagtatttttgcttgcagATTCACTCGAGGAAAATGACTGTGAGCTCCGATGTGAACTTTGAGGAGCTGGCGCGCTCCACGGACGACTTCAATGGTGCTCAACTAAAGGCCGTGTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA
  ggcttac  putative branch site (score: 3)
                                          ctttctacc  putative PPT
         tacttagttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatacttgacacgggcatgcacatgcaaagtgattatgaactgggtaaagcctcttgtttgcaatgacgtgcttgttcagtcatatgatttacgtagaggcttactacttagttttcattttcaataattttcttggactttctaccgcagATTCATTCGAGGAAAATGAATTTAAGGCCTGATGTCAACTTTGAGGAGTTGGCTCGCTCAACAGATGACTTTAACGGAGCTCAATTGAAGGCTGTGTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG