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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag

Basic information

species Physcomitrella patens
transcript PP1S83_25V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 5'ss of exon 10
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag
  || ||||||||||||| ||||| || || || || ||||| || ||||||||| |||||||||| || || ||||| |||||||| ||||| ||||||||     || | ||| ||||     | |    |  |  | |  |||| |          | | |||   ||| || | || |  |               
ACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAATGAGAGTCGCTGGTGTTCTTCATATCTTTCAGTTTGAAACTAAGCAGgt--tagttttaaatctctaccaggaaat---aattcatactatgtgta---------ggctgtgaaataaccatctgatatttag--------------

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G423861_T02 (Zea mays), 5'ss of exon 10
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatct---attcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag
 ||  |||| |||||||| ||||| || || || |||||||| || |||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||||||||     | | |  | |     | ||||| |  | ||  | | || |  ||    | | | | ||     ||| || |  | ||                 
ATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAATGCGAGTTGCTGGTGTCCTTCATATCTTTCAATTTGAAACAAAGCAGgtattctaaagtttcgaggcaatagttcataatgcatctgatcctgt-tatatcatctataactgatagaataaccatgttttttag----------------

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GRMZM2G070273_T01 (Zea mays), 5'ss of exon 10
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag
  |  |||| |||||||| ||||| || || || |||||||| || ||||||||||| || ||||| || || ||||| ||||| || ||||||||||||||||    ||| ||  |    ||  ||| |  |  |  | | |    |||    || || | ||   | | |  ||  |   |  ||  ||||  |    
ACTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTCTTCTTTAAAATGCGGGTTGCTGGTGTTCTTCATATCTTTCAATTTGAAACAAAGCAGgtat----tctaaagcttcgaggcaatagttta--taatacagcc--gatcctgttata-tcatccat-agctgttagaataacgatgactttttag---

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA01G35950.1 (Glycine max), 5'ss of exon 12
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatc--tattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagt-caacaatttaatgtaaaatccctttgaaacag------------------
|||| | || || ||||| ||||| || || || ||||| |||||||||||||||||||| || || || || || || |||||||| ||||||||||||||||    || || |  | |  |   |     |||  |  |    |  |  |||    ||| | ||   | ||  | |||   || |  |    ||   |                     
GTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGAGTTGCAGGTGTTCTTCACATATTTCAGTTTGAAACAAAGCAGgtattagcatgctcagggacattctactctaccaatttcttaatttcggcctttggacttattcatatcttcattactttggagttattttatattattagtattttatcattctttgaag

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: GLYMA11G09480.1 (Glycine max), 5'ss of exon 12
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatc--tattcttaatgtctatggtcatactcaagcttctgcggtgtggattta-attttagttatgagt-caacaatttaatgtaaaatccctttgaaacag------------------
 ||| |||| || ||||| ||||| || || || ||||| ||||||||||||||||| || || || || || || || || ||||| ||||||||||||||||    ||  | |  | |  ||  |     | || |  |    |     |||  | || | | ||   | ||  | ||| | || |  |   |||                         
ATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAATGCGGGTTGCAGGTGTTCTTCACATATTCCAGTTTGAAACAAAGCAGgtattggcatgttcagggacactgtactcttcctagttcttaatttcgacctttggacttgactcatatcttcattactttgaagttattttattttattggtattttatcattctttgaag

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaa--atccctttgaaacag
  | || || |||||||| |||||||| |||||||||||||| ||||| |||||| |||||||||| || || || || ||||||||||| ||||| ||||| |  |   | | | | | |||               |    | || |   ||||    |||||||  |   | ||   ||||    |   |||| |    
ACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAATGAGAGTCGCTGGTGTTCTTCACATATTTCAGTTCGAGACAAAACAGgt-ttaaacatcactatttgtgg----------atcattatattatgaagc-aattcc--ttatgagatattcaatttgggtaacttgtatgtttgtag---

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 5'ss of exon 11
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattctt---aatgtctatggtcatac---tcaagcttctgcggtgtggat------ttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag----------------------
  |  ||||||| ||||| ||||| || || || ||||||||||||||||| ||| |||| || || ||||| || || || ||||| ||||| || |||||   || ||||   | | |||||    |||    | |   || |   || |   |      ||  |||||  |||   |        ||    |||||   | |   | ||                      
ACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGATGAGAGTTGCAGGTGTCCTCCACATATTCCAGTTTGAAACTAAACAGgttcttaatcttttgagtttctatatgtatatatataacatttttagagttttagtctcttttttcttttatgtattccttgtttgcctatcaaaaaattattatttgatagagttctattccattttatgcag

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: EFJ30174 (Selaginella moellendorffii), 5'ss of exon 11
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatg--gtcatactc-aagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag
| || |||| |||||||| ||||| ||||| || || || || |||||||||||||| || || |||||  | || ||||||||||| ||||| || ||||| ||| || |   | ||  ||  ||  | ||| ||  |||||  |                                                         
GCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgtct-ttgtggctttccgtgtagttcttctctaaatttctgtcgcag------------------------------------------------------

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: EFJ06058 (Selaginella moellendorffii), 5'ss of exon 11
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatg--gtcatactc-aagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag
| |  |||| |||||||| ||||| ||||| || || || || |||||||||||||| || || |||||  | || ||||||||||| ||||| || ||||| | | || |   | ||  ||  ||  | ||| ||  |||||  |                                                         
GCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAATGCGTGTGGCGGGAGTTTTGCACATTTTTCAGTTTGAAACTAAACAGgtgttt-ttgtggctttccgtgtagttcttctctaaatttctgtcgcag------------------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAATGCGAGTCGCTGGAGTCCTACATATTTTTCAGTTCGAAACAAAGCAGgtatctattcttaatgtctatggtcatactcaagcttctgcggtgtggatttaattttagttatgagtcaacaatttaatgtaaaatccctttgaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA