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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG

Basic information

species Physcomitrella patens
transcript PP1S228_18V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
aggggtatcaggacctgaccaggt-cttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                    | || |||  |         |||||   ||    |  | |   |||  |||    |||| |   ||  |      |||||||  ||||||||||| || || ||||| || ||||| ||||||||| | ||||||||||||||||| ||| |||| |||||||| ||||||
-----------------gtaatgtacttccatttgacatgctgtcatcatattttaattggcaaatggttt----ctcatgtcataacacaaaa-ttgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os07g37560.1 (Oryza sativa), 3'ss of exon 13
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
    ||||  ||| |  | ||  |  |||  ||| |          |||    | ||| ||  || |   || | | |   || |||||    ||  ||||| ||  ||||||||||||| |||||||| ||||| || |||||| | ||||| || |||||||| ||||| |||||||| || || |||
----gtat--ggaacaaaacacattctttttaatat---------gaattttttcttc-taatatctcagttat-taacatttaactataccact-acagAAGAATGGTTTTGAGCAATTTTGTATAAACTATGCCAACGAAAGGCTACAACAGCACTTCAATCGACATCTTTTCAAGCTAGAACAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                    | |   ||| |  |  | |  || |  ||  |  ||   |   || |  ||  |    |     | |||  |  |||||||| ||||||||||| || || || || |||||||| |||||||||||||| |||||||||||||||||| |||| |||||||||||||||
-----------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctga----cattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 13
aggggtatcagg-acctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
   |    ||      ||      ||    || | |||  |   | || |   | | |  || | |   | |  |  |  ||   | |||     |||||||| ||||||||||| || || || || |||||||| ||||||||||||||||||||||||||||||||| | || |||||||||||||||
-cagaccccactcgtttgggatcctccggcactaggtctgcccccaaagttgtcatatattaaattgcatgtacttactggcgacattattacatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G057380_T01 (Zea mays), 3'ss of exon 13
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                |    |    ||| || |      |||  |   |   ||| | | | ||||  |  ||   ||  |||  |       || ||||| ||  ||||||||||||| |||||||||||||| ||||| ||| |||| || || |||||  | |||||  |||| ||  | || |||
----------------gtatggaatatttgcatt-----ttgtttagtactgatttacttggcatttcctcagttgtaatatttggttaaaccattacagAAGAATGGTTTTGAGCAATTTTGTATAAATTATGCCAATGAGAGGCTGCAGCAGCACTTCAACAGACATCTTCTCAAACTACAACAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA12G34780.1 (Glycine max), 3'ss of exon 16
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaa---atccacttttcgtagaattttttttgtctcaagctttactatggtt--cttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                          | | || | |  | |  ||     ||  |   ||| ||||     | ||   | |   |||| |||  ||   ||| |||| ||||| ||||| ||||| |||||||| ||||| ||||| ||| | ||||||||||||||||| |||||||| || |||||||| |||
-------------------------gtatgcagtttgtattaacgtgtttattgatgcttcatagatagactctttgttaatagtttattatttttattttgtagAATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 15
aggggtat-caggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttctt-gcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
    |||| |||    |    | || |||    |||     |    | ||  ||| || |||       | |  ||| |   |||| |||  ||||| | |||| ||||| ||||| ||||| |||||||| ||||| ||||| ||| | ||||||||||||||||| |||||||| || |||||||| |||
----gtatacagtttgtattaacgtgtttattgatgcttcat----agatagactctttgta-------tgtattctaatagtttattatttttctttgtagAATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 12
-------------------aggggtatca---ggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttac-tatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                   ||   | | |   |    ||     || |||  || | |||  | ||  | |  | ||||   |   |||  | |||   | ||  |   | |  | | ||||||  |||||||||||||| || |||||||||||||| ||||| || || |||||||| |||||||||||| | |||||| | || || |||
gtatgttatattatatgacagatcttttatatgtgtgtgtgtgtgtatttatcactatcc-ttatcctatttaattttttaaaatgtttgctctgttgtatgcggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA12G22300.1 (Glycine max), 3'ss of exon 14
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaa---atccacttttcgtagaattttttttgt---ctcaagctttactatggttcttg-cagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                          | | |||| |  | ||  | |   ||  | | |||  ||||| || | |     || |   |||  | |    |||  ||||||||||| ||||| || || | |||||||||||| ||||| ||| | ||||||||||| ||||| |||||||| || |||||||| |||
-------------------------gtgtgcaatttgtattgatgtatttatttattcttcaaagaatgttgtatacgtactgatagtttcttgtatcacttttcagAAAAACAGCTTTGAACAGTTTTATATAAATTATGCCAATGAGAGGATTCAACAACATTTTAATCGGCATCTGTTTAAACTTGAGCAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 14
----------aggggtatcaggacctgaccaggtcttttacaatgt-ccactgtcgaaatcc------acttttcgtagaattttttttgtctcaagct-ttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
               |  |||  | |    | |  ||||    | |  |||| ||   ||||      | ||||   |   |||  | |||   | |   |   | |  | | ||||||  |||||||||||||| || || ||||||||||| ||||| || || |||||||| |||||||||||| | |||||| | || || |||
gtatgttatattatatggcagatcttttatatgcgtttttgtgtatatcactatccttatcctatttaattttttaaaatgtttgctctgttgtatgtggtggattttatgcatgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAACAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA06G39740.1 (Glycine max), 3'ss of exon 14
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtct-----caagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                      || |   |        | |||    ||  |   |||  ||||| |||  |   |      |   | |  |||   | || ||||||||||| ||||| || || | |||||||||||| ||||| ||| | ||||||||||| ||||| ||||| || || |||||||| |||
----------------------gtgtggaatttgtattaatgtgtttatttatgcttcaaagaatgtttcatacgtactaatagtttcttgtatcactttttcagAAAAACAGCTTTGAACAGTTTTATATAAATTATGCCAATGAGAGGATTCAACAACATTTTAATCGGCATCTATTTAAACTTGAGCAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
----aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatc-cacttttcgtagaattt---tttttgtctcaagctttactatg------gttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
         ||| |     |  | |  |||||    || |  |   |  |  || |  | ||| |    |||    ||||| ||| |    | |||||       | | ||||||  ||||||||||| || || || ||||||||||| ||||| || || || ||||| |||||||||||| | |||||| | || || |||
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 12
--------------aggggtatcaggacctgaccaggtcttt-tacaatgtc-cactgtcgaaatccacttt--tcgtagaatttttt---ttgtctcaagctttac-tatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
              |    ||||   | ||  | |  | ||| |    | || |||  ||   ||||  |||  |  || ||| ||||   |   || | ||| | | | |  | | ||||||  |||||||||||||| || || ||||||||||| ||||| || || || ||||| || ||||||||| | |||||| | || || |||
gtatgtttatattaaactttatctacatctttctatatatttatgatttatctcaccatcttcatcctgtttgatattaaaatattttggctctactgatgctatgcattttatgcctgcagAGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTTAATCGTCATTTATTCAAGTTAGAACAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 14
-----------------------------aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtag-aatttt--ttttgt---ctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                                  |    | || |    | |   | | ||   | ||   ||    |  || ||| |||  ||| ||  ||| ||   || ||    ||||||   | ||||||||||| ||||||||||| || |||||||||||||| ||||| || ||||| ||||| ||||| |||||||| |||||||||||||| |||
gtatgctggtttttagtctccctttgcgttttactgcatgaacttacataagctatctgcacattacatcttctgtgtt-acattttgtaccaatgttaatttggtttgctgaataaatactatacatgttgcagAAAAATAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTCAACCGTCATCTCTTCAAGCTTGAGCAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------------------------------------------------------------aggggtatcaggacctg------accaggtcttttacaatgtccactgtcgaaat-ccacttttcg---ta-gaattttttttgtctcaagctttactatggttct--tgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                                                                                    |  | || ||     ||      |  ||  || |     | |   || | |   | ||| || | |   || |  | || ||  | |        ||| |  |||   |||||||||| || || ||||| || |||||||||||||| ||||| || ||||| ||||| || || |||||||| |||||||| |||||||||
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv19s0014g03640.t01 (Vitis vinifera), 3'ss of exon 14
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaag--ctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
               |   ||  ||   |  | | | |   |||    | |   |    ||  ||| |     || ||||    |||   |     || ||||| ||||| ||||| ||| | |||||||| ||||| ||||| ||| ||||||| |||||||||||||||||  | || || || || |||
--------------gtatacaattcacattta-tctgcttagtcatgtttctaatggaatatgattataacactcacaaggatcttatcttcaaattttcagAAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 13
----aggggtatcaggacctgacc--aggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgt-ctcaagctttac-tatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
         |||   |      |   |  |  |||   ||  || |  |      ||| | | |    || ||| |   |  ||| | |  |  |   ||| || |||| ||| || |||||||| || || ||||||||||| ||||| |||||||| || || || || |||||| | |||||| | |||||||||
gtatgatattatttagtttctgctgtaaataatttttcattccccccattc---cccattgtccccctaaatttataaatattcatgttacatattctgtttttccagAGAAATAGCTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGGTTGCAGCAGCACTTTAACCGTCATTTATTCAAGTTAGAGCAAGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ20281 (Selaginella moellendorffii), 3'ss of exon 12
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                                         ||||   | | ||  |  |||  ||     | |  |    ||| |||       ||||||  || |||||||||||| | || ||||| ||||| |||||||| || || ||||||||||| || || |||||||| || |||||||||
-----------------------------------------gtcg--gtgcgctagttttagttttcgcgattttactgagttttctac------tgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

upper sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                                         ||||   | | ||  |  |||  ||     | |  |    ||| |||       ||||||  || |||||||||||| | || ||||| ||||| |||||||| || || ||||||||||| || || |||||||| || |||||||||
-----------------------------------------gtcg--gtgcgctcattttagttttcgcgattttactgagttttctac------tgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG
                                              ttcttgc  CT-rich tract
              tagaattttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatccacttttcgtagaattttttttgtctcaagctttactatggttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA