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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG

Basic information

species Physcomitrella patens
transcript PP1S87_157V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g49430.1 (Oryza sativa), 3'ss of exon 2
--------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtt-tggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                                  | ||  ||  |      ||  ||  | |  |   | |    | || |||     |    || | | |  |    || |      |   |  ||    |||||||||||||||||||||||| ||||| |||||| || |||||||| | || |||||  ||||||| |||||||| |||||||| || |   | |||| 
gtaagcttaactactgataatccccaattccccaagaacctacttgaccaccattaaacacatagttctgttgatttatcaattaacatggaattctagcttattctctgataaatcatctatattggcacagCTAATGTATTTCATCGCGATCTAAAGCCCAAGAATATACTGGCAAACTCAGACTGCAAATTGAAAATATGTGATTTCGGACTTGCCCGAGCATCATTCAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 2
-tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgcttt--agCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
 || |        | ||| |      || |  |   |     || |    || |||| |||   |   |  ||||       | ||| | |     |||  ||| |||||||||||||| |||||||| ||||| ||| | ||||| || |||||||| ||||| ||||| |||||||| || |||||  |||| ||||| ||
ctgtactcagtgttctatgtttgtgtgattcctatttatcagtccatcctatttgtgactc---taattcctgactgatgcatcttttgatagctttttgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATCTTGGCGAATGCTGATTGTAAGCTCAAAATATGTGATTTCGGCCTTGCAAGGGTAGCTTTTAG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g04230.1 (Oryza sativa), 3'ss of exon 2
-------------tgaaaatgtaacta--tatttcaagaaga--------atagtggat---tatgatctaatgaatgtgtgtctcg---tttggatgttgacgtgcttc---tatttgggtga---tgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
             | |  || ||| ||    | |||  || |        ||     ||   |||  | |   |||  | | | ||     ||     ||   | | |||   ||| ||| | |   ||  | |||||||||||||||||| ||  | |||||||||||  || |||| ||  | || ||||| ||||| |||||||||||||||||||| || || || || | 
gttagtgatgaaattagcatctaattaaccttgtcaccaacagccacttcattccaaatctgtatactttgtggaagttatatttcaaccattaatcattactgagtttctgatatatggtttaacttgtctcagCTAATGTATTTCATCGTGACTTAAAGCCAAAGAACATACTGGCCAATTCAGACTGCAAACTGAAGATTTGTGATTTTGGACTTGCACGTGTAGCATTTAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 2
-------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
       ||| |      ||  || |||  |     | |  ||| || | || |  |  | |  ||  | ||   | || | | | | ||||||  |  |||   ||| ||||| ||||| || ||||| || ||||| ||| | |||||||| |||||||| ||||| ||||| ||||||||||| |||||  | || ||||||||
agtagcctgatatgactgctccatctcattatt--caatatattttgttatactagaatttta-ctgatatgacagctgtctttcat-tatttgtttactgc---agCAAATGTGTTTCACCGAGATCTTAAACCAAAAAATATTTTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTTGCAAGAGTTGCTTTCAG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G135904_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgt---gtgtctcgtttggatgt-------tgacgtgcttctatttgg--gtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                                                 |    ||   |||||||     |   | |||| | ||   || |||  | |   || | | |||  ||| |       | | ||||| ||    |    |  || |  |||||||||||| ||||| ||||| ||||| |||||| || |||| ||| | || ||||| |||||||| ||||| ||||||||||| || |   | |||| 
gtaagtatattagctagtaccaaccacatggtacctatcccatgtaccaaggcagtttatatatttgtcagactgttgtggttcatctgctcatggttatctagtttgttgttatgatatattatgataatgtgctccttgcggtctatattggtgcagCTAATGTATTCCATCGTGATCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGACTTGCCCGTGCATCATTCAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatagtgg-attatgatctaatgaatgtg-tgtctcgtttgg-atg-ttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
    | |   |     |   ||   |  |  |     | ||  ||  |    |   |  |  |  ||  |||  ||| |    | |   | | | ||  |  ||| |||||||||||||| |||||||| ||||| ||| |  ||||||| |||||||| ||||| ||||| ||||| |||||  | ||  | || ||||||| 
--tcattactaggggctcctaatctgtctgtttccgctgtgtccttttagtggcactaacatgcctgatatgactgatgcatctttcaatagcttat--tgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 1
-------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
       |     | | ||| | || ||   ||    ||   |     |   |  ||  ||   ||  | ||     ||| |    | |   | | | ||  |  ||| |||||||| ||||| |||||||| ||||| ||| |  ||||||| |||||||| ||||| ||||| ||||||||||| || ||  | || ||||||||
taggggcttctcttcttactgttttccagtgagttctgttagtggcagtggcactaacatgc--ctgatatga---ctgatgcatctttcaatagcttat--tgcagCAAATGTATTCCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTAGCAAGAGTAGCTTTCAG

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G306028_T02 (Zea mays), 3'ss of exon 2
-----------------------------------------------tgaaaatgtaactatatttcaagaagaatagtgga-ttatgatctaatgaatgtgtgtctcgtttggatgttgacgtg-cttctat-ttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                                                 | |  ||   | |||||    ||   | ||||  | ||    | |||  | |     |  ||   |   | | |||   | ||| ||   |   | |  |||||||||||||||||| || || ||||| |||||| || |||| ||| | || ||||| |||||||| ||||| ||||| ||||| || |   | || | 
gtaagtatattaattagtaccaaccacacagtacctatccaatctagcaagacagtttttgtatttgtcaaattgttgtgggctcatctgttcatggttatccagtttattattacaataatgtgatctttatgttctataccggtgcagCTAATGTATTTCATCGTGACCTAAAGCCCAAGAATATACTGGCTAACTCGGACTGCAAACTGAAAATATGTGACTTTGGTCTTGCCCGTGCATCATTTAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatag--tggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
       ||   || | | ||    || | |  | | | ||| | |  |   |   |   || | ||    |     |   |   | |   || |  |  ||| |  || || ||||| ||||| ||||| |||||| |  | || || ||||| ||||||||||| |||||||||||||| ||||| || ||  | |||| 
-------gttgttagactccacattgagtggacttgttaatggtttgttacgt---tacttcttgtgagcttcagtttctatgcttgttcttggttttgcagCAAGCGTCTTCCATCGGGATCTTAAGCCCAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
----------------------------------tgaaaatgtaactatatttcaagaagaatagtggattatgatctaa-tgaatgtgtgtctcgtttggatgttgacg-tgcttcta----tttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                                  |  |    |||      ||    |    || ||  |||| ||  ||   |||   ||  ||   ||    |||  | || || ||    |||   ||    | |||| ||||||||||| || ||||| |||||||| ||| | || ||||| ||||| ||||| ||||| |||||||| || || |||||  | |||||||||| 
gttatgatctttatatttagctagtttttatttttagattcctaatgcagctttttcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgattttaaactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctt-tagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                            ||     || | ||  | |   ||  |||  |   | | || | |    ||   ||     |  | |||  ||| ||||| |||||||| ||  | |||||||| ||| |  | || || |||||||||||||| ||| | |||||||||||||||||||| ||  | || | 
---------------------------gtatcc--ttgtaattaagtccttgactgttgctgatag-tgataataaactaaaataacattttttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatagtggattatgatc-taat-gaatgtgtgtctcgtttggatgttgacgt---gcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                            || || ||  | ||  |||     |   || ||  ||| |||   ||  |    ||  | | |   |  |  |  ||| || || |||||||| ||| | |||||||| ||| |  | || |||||||||||||| || ||||| ||||||||||| |||||||| ||  | || | 
---------------------------gtattgcatccttattataaccaggtccttgacttttttagatagagatattaaactagtgtatcatttttcttgcagCAAACGTGTTTCATCGTGATTTGAAGCCAAAAAATATTCTTGCTAACGCTGATTGCAAACTAAAAATATGTGATTTTGGGCTTGCTCGAGTTTCATTTAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatagtgg-attatgatctaatgaatgtgtgtctcgtttggatgttgacgt---gcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                      | |   ||     |||||||     |   |   || ||  ||| |||  |||  |    ||  ||| |   |  |  |  ||| ||||| |||||||| ||| | |||||||| ||  |  | || |||||||||||||| || ||||| ||||||||||| |||||||| ||  | || | 
----------------------gtattgtatccttattatgacaaggtccttccttgacttttttagatagtgatattaaactagtatatcatttttcttgcagCAAATGTGTTTCATCGTGATTTGAAGCCAAAAAACATTCTTGCTAACGCTGATTGCAAACTAAAAATATGTGATTTTGGGCTTGCTCGAGTTTCATTTAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
            || |  |   ||  ||||     | ||    || |  | || | |    | |   | |  |  | ||| | |||         || ||||||||| |||||||| ||||| || || || ||  |||||||||| ||||||||||| || || || |||||||||||||||||  | || || |||| 
----------gtta-agctagcgagcaataaaatttcattgattagtataagtttatgat-tatctttctgaaaatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatagtggattatgatctaat-gaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
       ||   |   |||||   | | ||  |  | |   | |  | |  | | ||||  |  |||    | |      | | | ||| |  |  |  ||| ||||| |||||||| ||| | |||||||| ||| |  | || || || || |||||| |||| |||||||||||||| |||||||||||| | |||| 
-------gttggtgcttttcagagatattatagcctcaccgtttgtttgcttttatgtcctgaatggccactaataaaaattt-tatggtt--tcttccagCAAATGTGTTTCATCGAGATTTGAAGCCAAAAAATATTCTTGCTAATGCCGACTGCAAGTTGAAGATTTGTGATTTTGGGCTTGCTCGGGTGTCATTCAA

upper sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ38694 (Selaginella moellendorffii), 3'ss of exon 2
tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                                 | ||   |  |  ||  | |   |||    ||     |    || ||||  |  | |  || |  ||| ||||| || ||||| ||| | |||||||| ||  |  | || || || || |||||||| ||||| |||||||||||||||||||| || ||||| | 
---------------------------------gtttgcaacttcttggttat---tcttcagtgtgcaattctctgtttcttctgtgctcttgatgcagCGAATGTGTTCCATCGAGATTTGAAGCCAAAAAACATTCTTGCGAATGCCGACTGCAAGCTAAAAATCTGTGATTTTGGACTTGCTCGAGTTGCTTTTAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162191647|gb|FC367692.1|FC367692
EST:     TCAATTCTTTTTGTACCAGCTACTGAGGGCTCTCAAGTATATCCATACAG                         CTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTG
genomic: TCAATTCTTTTTGTACCAGCTACTGAGGGCTCTCAAGTATATCCATACAGgtgggcgtca ... gatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTG
EST: gi|162257300|gb|FC433383.1|FC433383
EST:     TCAATTCTTTTTGTACCAGCTACTGAGGGCTCTCAAGTATATCCATACAG                         CTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTG
genomic: TCAATTCTTTTTGTACCAGCTACTGAGGGCTCTCAAGTATATCCATACAGgtgggcgtca ... gatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG
                      tgttgac  putative branch site (score: 3)
                                 ttctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaatgtaactatatttcaagaagaatagtggattatgatctaatgaatgtgtgtctcgtttggatgttgacgtgcttctatttgggtgatgctttagCTAATGTATTTCATCGCGATCTCAAGCCAAAGAATGTATTGGCAAACGCTGATTGCAAGCTGAAAATTTGTGATTTTGGACTTGCTCGGGTGGCTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA