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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgggtgacatgagccaacagttggaagaagtatcagggtttcaatttagaggcgaaccgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC

Basic information

species Physcomitrella patens
transcript PP1S44_339V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 4
---ctgggtgacatgagccaacag-ttggaagaagtatcagggtttcaatttagaggcgaaccgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC
    ||    |  | |       | ||| |       | ||| |||    ||||  ||  |       ||  |  |||        |   || |     | ||||||| |||   || || ||  |  ||  ||| || |||||||| || |||||||| ||||| |||||||||||||| ||||| ||  | ||||| ||| |
tatttgcacaaattcaatatgtggattgcattgtactttaggattt--gcttagttgcataatttgtttgttc--taactgtgttattctgatccaaaattcagGTACCACTTGTGCTACTGTATTGACTAAAGCAATATTTACTGAGGGGTGCAAGTCTGTTGCTGCTGGCATGAATGCAATGGATTTAAGGCGTGGTATTTC

upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 4
ctgggtgacatgagccaacagttggaaga--agtatcagggtttcaatttagaggcga--accgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC
 ||       | | |||||  |  |       |||| |   |   |||||||  ||    |||   || |||  || |    ||| |    || | ||||||||| || ||   ||| ||||| ||| | ||||| || ||||||||||| ||||| || ||||| ||||| |||||||| |||||| || | ||||| || | 
-tgaagactgtaaaccaactatcagcttgctggtattatc-taataatttaggtgctgttaccatgaaagaatattgagggaacatt--tcaattgttttgcagGAACCACGTGCGCTACAGTCCTTACACGAGCAATATTTACTGAAGGCTGCAAATCAGTTGCGGCTGGAATGAATGCAATGGACCTGAGGCGTGGTATAAG

upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 4
-------ctgggtgacatgagccaacagttggaagaagtatcagggtttcaatttagaggcgaaccgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC
        |   |||||   ||  ||   |  | |  || || | | || | |||      |     || ||  |   | | |    | |   ||   |||   ||||||| ||    || ||||| ||| | ||||| || ||||||||||| |||||||| ||||| ||||| |||||||| |||||| |  |  | || ||  |
agaatggttttatgaca-atgcatacttgtctacgttgtctctgtggtttattttgtttctg--ttacacatagat-ctgatcccttatttttgatgattt---cagGTACCACCTGTGCCACAGTCCTTACCCGAGCAATATTTACTGAAGGGTGCAAGTCGGTTGCTGCTGGAATGAATGCAATGGACCTAAGAAGGGGTATCTC

upper sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 2
ctgggtgacatgagccaacagttggaagaagtatcagggtttcaatttagaggcgaaccgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC
                                    |   |||    |  ||      |     |     ||    | || ||    | ||  | || ||| || |||  |||||| ||||||||||| || |||||| | || ||||| ||||| || || ||||| |||||||||||||||||||||||||| || | 
------------------------------------gtacttcttcctctagtt---tctttcttttctcttttcttaactgt----atctggtgtgtagGAACTACTTGCGCAACTGTGCTTGCTCGCGCAATTTTTGCAGAGGGTTGTAAGTCTGTGGCGGCTGGAATGAATGCCATGGACTTGCGCCGTGGTATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagaggcgaaccgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC
                                  cagtaac  putative branch site (score: 2)
                                            cttttttgc  putative PPT
                                          aactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgggtgacatgagccaacagttggaagaagtatcagggtttcaatttagaggcgaaccgcaaatgaacgttaaactgacagtaacgaacttttttgcagGTACAACTGCCGCAACAGTGCTTGCTCGAGCCATTTTTACTGAAGGTTGCAAGTCCGTTGCAGCTGGCATGAATGCCATGGACTTGCGCCGTGGCATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA