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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttgaaagacaatgtgattttatgttttttttcgagatggatgcatgatgcatacactgttgggaatcttttctcaacacctcgttcaatccacagGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAG

Basic information

species Physcomitrella patens
transcript PP1S141_3V6.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S141_3V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
tttttttgaaagacaatgtgattttatgttttttttcgagatggatgcatgatgcatacactgttgggaatcttttctcaacacctcgttcaatccacagGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAG
       | | |    | | |  | ||||    | |    ||| |||  || |  ||    |  ||  ||  ||| |   | |    ||        |||||||| |||||||| ||||||||||| || |||||||| || || ||||| || || || || || |||||  | ||| | |||||||| || |||
-------gtatgcatgtcttagctgatgtacagtattaccatgcatg--tggta-atttgttcatgtcaacttttgcatgaaattatgt--------cagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG

upper sequence: PP1S141_3V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GLYMA15G26120.1 (Glycine max), 3'ss of exon 7
tttttttgaaagacaatgtgattttatgttttttttcgagatgg-----atgcatgatgcatacactgttgggaatcttttctcaac--acctcgttcaatccac--agGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAG
                        | |||  || ||  |||||      |||| |  |  ||  | | |||   | | ||   ||||  |     |||||   |   |||| || |||||||| ||||| ||||| || |||||||| || ||||| || || |||||||||||||| |||||     ||||||| ||  |||||
-----------------------gtgtgtgattctttaagatgattcatatgccttttttatttatt-ttgtatagcattgagcaaccaatggttttcaacggatgtagGGATATTGGATGGTCAAGCGAGCTGTAGGAACAAAAGCTTGCCTACTAGGGAAAGCTGTCACTTGTAAATACTTTAAACAAGATAATTTTTTTGAG

upper sequence: PP1S141_3V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
tttttttgaaagacaatgtgattttatgttttttttcgagatggatgcatgatgcatacactgttgggaatcttttctcaacacctcgttcaatccacagGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAG
              || |  | | |    || |  |    |  ||   ||  |  |   | |            || | | |  |  | | |||| |||||| || |||||||| ||||| |||||||| |||||||||||  | || ||||| ||||| || ||||| ||| || |  | ||||||||  | |||
------------gtaaagaaactctgctcttctcgtttccactgaaatatagtaaacttagtcaca--------ttgtaaccgtcatggtgaatc-acagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgatgcatacactgttgggaatcttttctcaacacctcgttcaatccacagGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAG
                                      cctcgttc  CT-rich tract
                       aatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttgaaagacaatgtgattttatgttttttttcgagatggatgcatgatgcatacactgttgggaatcttttctcaacacctcgttcaatccacagGGTTACTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCCTGTCTACTGGGTAATGCTGTCACTTGTAATTACTTGCGCAAAGATAACTTCCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - -tgatgca