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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataataattagaaacttgctcaacctcttatattttggtatctaatttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG

Basic information

species Physcomitrella patens
transcript PP1S14_82V6.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
tataataattagaaacttgctcaacctcttatattttggtatctaatttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG
                                   |  || |||    | |  | | | |  |      ||| |   |   | ||||  ||   | ||||||||||||||||||||||||| || ||||| || |  ||  | ||||| |||
----------------------------------gtaagtgtctgtcctttaagctctctggtgccc--ttttatggatctaattttcgtcatgt-acagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG

upper sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 25
------tataataattagaaacttgctcaacctcttatattttggtatctaatttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG
            | ||   || ||| |||   | ||| || |       |   ||| | ||| | |  ||||     | ||   |||  ||  |   | ||  |||||||||||||||| ||||||| || ||||||||| ||||  | |||||||||
ctcaacctcttcactttacaaattgatcataatattagatgtccactgtttcattgctggttatcttgtata-----ttaatttctc-tttgatgattttttgcagGATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATG

upper sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 25
-----tataataattagaaacttgctcaacctcttatattttggtatctaatttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG
      | |  | ||   || |||  ||   | ||| || |       |   ||| | ||| | |  ||||     | || | |||  |  |    | ||  |||||||||||||||| ||||||| || ||||||||| ||||  | |||||||||
atctcaacatcactttacaaattgaccataatattagatgtccactgtttcattgctggttatcttgtata-----ttaatctctctttgatgggttttttgcagGATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATG

upper sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 25
tataataattagaaacttgctcaacctcttatattttggtatct--aatttgtttgttttttaatataa-gatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG
  |   | ||     || |    | | ||  ||| |   ||  |  | || |         |   | ||  |||||  | |  || || |||| |     ||||||||| |||||| |||| |||||||||||||| |||||  | ||||| |||
agtgtcacttcagttctgggcatagccctggtatctatttaattggacttagcacaaaccctgtgacaacaatttctcataaccaattcttttgtg---gcagGATACGTGATGATATTGAAAAGGAAGATGCTTTCCGAGGCCTATGTGCCATG

upper sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 25
tataataattagaa-acttgctcaacctcttata-ttttggtatctaatt---tgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG
 ||   | | | |  || |  |  |  |   |||  ||||    || |      |    || |||  ||  || |    || ||  ||   ||    | |  ||||||||| |||||| |||||||||||||||| || || ||  | ||||| |  
-attggactcatactaccttttacatatgccataactttgcctgctgagcacaggcccattcttttttaacagttcattaataccaacaagtt----catggcagGATACGTGATGATATTGAGAAGGAAGATGCCTTCCGTGGTCTATGTGCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG
                               cactcac  putative branch site (score: 2)
                               cactcactttttttct  CT-rich tract
     tttgttttttaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataataattagaaacttgctcaacctcttatattttggtatctaatttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT