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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaatctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 14
gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaat--ctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG
                 || || ||   | |||  | |     | ||   ||| | |  ||| |   |   | ||||||   ||  ||| ||   | |||   |  ||   ||  |||||||||||||||| ||||||||||||||||||||  ||||| ||||||| ||  | ||||| ||    || || ||  | || ||||||
-----------------attctattctctgaaatctgattt--gtttaatttttttagcatccaagttgatttttttttggtttatgta-tagcataatttaatactttcttgattgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACCATAACAGATCTCTTTCTTCAG

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 14
gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaatctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG
      ||| ||    |||| || ||   ||    || |   |     |||   | ||  |    | | |  | |||   ||   || | |   | |||| |||||        ||||||||||||||| ||||||||||||||||||||  ||||  | || || || || ||||| ||    || |||||  | || ||||||
------ctatattgtttatgatgcttgcctagt--tacctttatacaatatcaattatcttgc-tagtttactcttttatttgtttatttagaac-ttgtttcatt--------gcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTACAACACAATAACTGATCTCTTTCTTCAG

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 12
gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaatctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG
          ||    |||| || ||   ||    || |   |     |||  || |||   | | |  |   | || | ||   |  | || |      ||| || | |   |||||||||||||||| ||||||||||||||||||||  ||||  | || || || || ||||||||    || || ||  | || ||||||
---------tattgtttatgatgcttacctagt--tacctttatacaatat--ctaatatcttgccagtttactctttttttatttgtttatttag--aactcgttttat---tgcagGGTGCTGTAAATTTTGCTCTGATGATGTCTCAAATGGAGGGGGGTTGCCCTGTTGACTATAACACAATAACCGATCTCTTTCTTCAG

upper sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 14
gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaatctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG
  |  ||| ||      ||   |||| |||||   |        || | ||    | | || |    | | |  ||||| |  ||||   || |  |     | || | |   ||||||| |||||||| ||||||||||||||| ||||  ||||| ||||||| ||  | ||||| ||    || |||||  | || ||||||
--atctctgaa------atctggtttgtttaagtttt-------gtagcatccaagttgattttttcttt-tagtttatgtatagtaagtatatt-tcaaaactttctttat-tgcagGGAGCTGTAAATTTTGCTCTGATGATGGCTCAAATGGAAGGAGGATGCCCCATTGACTACAACACAATAACTGATCTCTTTCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG
                      tactaat  putative branch site (score: 1)
        ttttttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttctaaatgacatatgctgtttctttaaaaataacccaaggttgtatttctgataatctacaatctgttttttatcttcagtactaatgtcattgtctcattatgtgcatgcagGGTGCTGTAAACTTTGCTCTGATGATGTCTCAGTTGGAAAGAGGATGTCCAGTAGACTATAATGTTATCACTGACTTGTTCCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG