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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG

Basic information

species Physcomitrella patens
transcript PP1S79_74V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G34610.1 (Glycine max), 3'ss of exon 2
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG-
                     | || ||| |    | ||  |||||||| | | |   || |  |   | || | |  ||||   |||||  | |    || |    ||||        | |||     |||           ||||| ||||||| ||  |||| |||||||| ||||| || || ||||| |||||||||||||| ||||| ||||| ||  | || |||||  |  || ||| 
-----------------tatgtattgttgaa--caaaaattttaaattttgctacccttcaaaatcatgtgt-tgtcttgag---gtaatttatc----atactatgtttt--------ttttggcttttat----------tagGTGATGGTGGTTGATGCTGAGGCATACACATATGATGATGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATC-ATTGCGAGGC

upper sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G02360.1 (Glycine max), 3'ss of exon 2
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG-
                     | || |||      | |   ||||||||    |   ||  |   |||||   | || |    | |||||  | |  |||    | |||||    ||  | ||                    ||||  ||||||| ||  |||| |||||||| ||||| || || ||||| |||||||||||||| ||||| ||||| ||  | || |||||  |  || ||| 
-------------------tgtattgttgtgaacaaaagtattaaattt--gctacccttcaaaatcagatggtgttgtctttaggtaatttatc--atactaagtattttgg--catttatt--------------------agGTCATGGTGGTTGATGCTGAGGCATACACATATGATGACGAGGTGCTTAAGAAAGCAGAAGCTATGGGCAAGCCTGGGCTTGTAGAAATC-ATTGCGAGGC

upper sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G15400.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG
                                | ||  |  ||    ||  | |  |     |||| ||   ||||  |  |||    || |     ||   |   | | ||| |    |  |  ||| | |           |||| |||||||| || |||||||||||||| || || ||||||||| | |||||||| ||||| ||||| || || ||  |  | || ||  |    ||  
--------------------------------tgtatgaatttt--ctttaagtgtttagtgcgtttagctcatttcttttgcagtctattgtttgaatcatcacaactgtaattataatact-ttgcttct----------tagGTTGTGGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCCATCCGAAAC

upper sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G15430.1 (Arabidopsis thaliana), 3'ss of exon 2
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG
               |||     |||  | ||||||   | ||  | ||   |  | |    | ||   ||| | ||  |    | | |||    || ||      |||||     |    ||||| | ||             ||| || ||||| || |||||||||||||| || || ||||||||| | |||||||| ||||| ||||| || || ||  |  | || ||       || |
---------------aacag---ttacagtagtttat--cgttggaatttagtatgccatttcttttgaagtctgtt--gcttgaatcatcacaactgta------atttt----tatactttgcttctta-------------gGTTGTAGTGGTTGATCCTGAAGCATACACTTACGATGAAGAAGTGATCAAGAAAGCTGAAGCAATGGGGAAACCGGGACTCATTGAGATCAGTCCGAAAG

upper sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv03s0180g00050.t01 (Vitis vinifera), 3'ss of exon 2
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG
                                 ||  |    |        |     ||| || | |||   || | ||||    ||   |      | ||   ||||  |   |    | |     | |||   | |  | ||||| || ||||  ||  |||| |||||||| ||||| || |||||||| |||||||||||||| ||||| ||||||||  | ||||| || ||   ||| |
---------------------------------ttgaatgtgtggggaggaa---aactcaacttccagcccatctgctgaatgtgtttcc---ttcagataatgcatcatgggttgtcttt-----catatgctcttttt-cagGTTGTTGTGGCTGATGCTGAGGCATACACTTATGATGATGAAGTGCTCAAGAAAGCAGAAGCTATGGGGAAGCCAGGGCTTGTGGAGATCTATGCCAAAG

upper sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ38153 (Selaginella moellendorffii), 3'ss of exon 3
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG
                                                                                  ||   | |||| | || | |    ||   |||  |    |    || |       | |   ||||||  ||| | ||||| || |||||||| ||||| || |||||| | |||||||| ||||||||||| ||||| ||  | ||||| || ||  ||||||
--------------------------------------------------------------------------------gtcagccagtcgagcttaga-gtttgataagaaactaaagctcaaagctt-----tgttccatagGTGGAAGTGATCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCCGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG

upper sequence: PP1S79_74V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ15766 (Selaginella moellendorffii), 3'ss of exon 3
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG
                                                                                  ||   | |||| | || | |    ||   |||  |    |    || |       | |   ||||||  ||||| ||||| || |||||||| ||||| || |||||| | |||||||| ||||||||||| ||||| ||  | ||||| || ||  ||||||
--------------------------------------------------------------------------------gtcagccagtcgagcttaga-gtttgataagaaactaaagctcaaagctt-----tgttccatagGTGGAAGTGGTCGACCCAGAGGCATACACTTATGATGACGAAGTGATCAAGAAAGCGGAAGCCATGGGAAAGCCTGGCCTTGTGGAGATCTATGGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG
                attttaaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcatattcatttaactcatcttattgcagtttacaaccttaaatttcgattcgtctcgacgttcagagtattttctgagcaagtaatcgaccctatatgcggcattttaaatcacgtgttgctgcgtataaacatgctgcagGTGGTGGTGGTGGACCCTGAAGCATACACCTATGACGAAGAAGTGCTGAAGAAAGCAGAAGCCATGGGTAAGCCAGGTTTAGTGGAAATTTACAGCAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG