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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG

Basic information

species Physcomitrella patens
transcript PP1S47_303V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 4
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                   || | |    ||     | |||| | |  ||      ||         |    ||| ||   ||     ||   |  |    |||| ||  | | ||  || || ||  | ||||   |||| |||||||| ||  | ||||| ||||||||||| || |||||||||||||||||   | | |
-----------------------------------gttagtgttcttgcttgtgcctataaaacaatttggattttgtttggctataaataatgc--ctgtaactacatttctctgtagGATTTTGATTACAATGAGTTAGACGCTGTTCTGCAATATTATCCTCACGGTTATCATGGAGTTGACAAAGACGGGAGACCTGTTTATATTGAAAGGCTTG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G05980.1 (Glycine max), 3'ss of exon 2
gt-tttggatcctggtgccatgattt-----agcatcttttgtaatttacttttaagattcctacacatgaacaaaattt-acaggaatttgcggatactgag--gctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
|| ||||  |  | |  | ||||| |     || ||     | ||| |     | |   ||    |  | |  | | |||         ||     |||| |   | | |  || | ||  |    |||| ||  | ||||  ||| | ||   ||| |   ||||||||||||| ||||| ||||| ||||| ||||| ||| |||| ||||| ||||||   || |
gtatttgtgtttttgaacaatgatatttgtgagaattcaggggaatgtgacccttattctcacttatttaattatagttttgttcctccttctatttacttaattggtgccttttttatact----agGATTTTGAATTCAAGGAACTCGAAGAAGTCCTGCAATACTATCCTCATGGACATCATGGAGTTGATAAAGATGGACGACCAGTTTACATTGAGAGAATTG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 3
----gtt-ttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaat-ttgcggatactgag--gctcctgt----tatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
    ||| |  |||         || ||  |     ||| ||   |    ||| |  ||    ||  || ||    |||     |   |||   || ||      ||   ||    | |  |  |    |||| ||  | |||   || ||| ||  ||| |   | |||||||| || ||  | |||||||| || || ||||||||||||||||||||||||  | |||
gtgagttatccgatttgaaaaatataatcaacttattttggttgatcctgtttta--tttgatcaactgtactgtttttttgaaatcgttgttcatgctatactactttggtttcctgtctttctctttagGATTTTGAATTCGGTGAGTTGAATGAAGTCCTGCAGTACTATCCACATGGTTATCATGGTGTGGATAAGGAAGGAAGACCTGTTTATATTGAGAGGTTAG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G36490.1 (Arabidopsis thaliana), 3'ss of exon 2
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatt-tgcggatactgagg-ctcctgttatg-atgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                          | ||  ||  || | ||     | | ||   | |  |||| |   | |    || |  | |  | | |     ||   ||| || || ||    |||| ||  | ||||  ||| | |||  |||    |||||||| ||||||||||||||||| |||||||| |||||| ||||||| || ||||||  | | |
--------------------------gtatgattattattctagaggaacgttttgcagatttgaaaatggtctctttgagtagtactaacattctcttctttggttttgtatatttttaagGAGTTTGATTTCAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTTGACAAGGAAGGACGACCTGTGTACATTGAGAGGCTTG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G21540.3 (Arabidopsis thaliana), 3'ss of exon 3
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                      |     |  ||||   ||   ||| |     | || |   | |  ||| | |             ||| ||     |  |  |      || || |||||||  | ||||  ||  | |||  ||| |  || ||||| ||||||||  ||||||||||||||||||| ||||| |||||||| ||||||  | |||
---------------------gtcctaaacattttaagatcatcttctttttcttctcctt-taattaaagtct-------------gatcct-----ttttacttcttctttcaaaagGACTTTGATTTCAAGGAGATTGATGAAGTCCTCAAGTACTACCCTCAAGGTTACCATGGTGTTGACAAAGATGGAAGGCCTGTTTACATTGAGAGGCTAG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                        |   |  |  |  | |||  || | | || |    |  || |      ||  |   | | |    ||||     |  | |  |  | |     |||| ||  | || |  ||| | |||  |||    |||||||| ||||||||||||||||| || ||||| ||||||||||| || || ||||||  | |||
-----------------------gtgtgaattcatagagtttctttatga-atgcaagaaggtgcattgtggttgaaaacaat-gttcttactcttttttttttctttgtatctcttagGATTTTGAATTTAAGGAAATTGATGAAGTGTTGAAATACTACCCTCAAGGACACCATGGAGTCGACAAGGAAGGAAGACCGGTGTACATTGAGAGGCTAG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT4G39180.1 (Arabidopsis thaliana), 3'ss of exon 4
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaaca-gGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                        | || |  |||  ||       |||    |  ||       | ||    | || | | | || |     | ||   || ||||||  | ||||  ||| | ||   |||    || || ||||| |||||| | |||||||||||||| |||||||||||| | |||||||||  | |||
---------------------------------------gtgacatcaaaggctcacttttttgactctatgttttgtctctgtgtctct-ctaatgtttctatctctttcttattcaagGACTTTGATTTCAAAGAAATCGAAGAAGTGGTTAAGTATTATCCACAAGGATATCATGGTGTTGACAAGGAAGGAAGACCTATCTATATTGAGAGGCTAG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                |   | |  |  |||||| |    |    ||     |  ||||     || ||  | |  | |   ||    ||||    | || |||| ||  | ||    || || |||  |||||  |||||||| ||||| ||  | ||||||||||| ||||||||||| |||||||| |||||     |||
-------------------------------gtgaattacatgtttttaaaaaaaatcttaatatgttacttttaatctcatgtgatggttttaa---tctcaatatgtgtgttaatagGATTTTGAATTTGAAGAGTTTGATGAAGTTCTGAAATACTACCCTCATGGTTATCATGGTGTTGATAAAGAAGGAAGGCCTGTTTACATTGAAAGATTAG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------gttttggatcc---tggtgccatgatttagcatcttttgta------atttacttttaagattcctacacatgaacaaaatttacaggaatttgcgga------------tactgaggctcctgttatg-atgttga--acagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                 |||  |||   ||     | ||  ||   |||| ||||      | ||  | ||  ||| |   ||  | | ||   | |  |  | ||   |||              || |   |  |  |||| ||||  |    |||| ||  | |||   ||  | ||   ||||    ||||||||||||||||  | ||||| ||||| || |||||||||||||| || |||||     | |
gttaggagtcatttatttaagtttgaaacctgcttgtttccatatgaaaaaaagaagtaatttcttgtgtacaacatacttggtatttggatgcaagcatctaatcattctctggattagttgatggaatcaatatctaactcttataattttactatgtatgtgaatggtagGATTTTGATTTCGAAGAGCTTGAAGAAGTTTTGCAATACTATCCTCAAGGCTATCATGGAGTTGATAAGGAAGGAAGACCTGTCTACATTGAAAGACTTG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 2
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                             | |   || | |||||||   |  |  | || |  |  |    |||||      |  |     ||  |     ||| |    |    ||||||||  ||||  | || ||||||   ||||  |  ||||| ||||| ||| | ||||||||||| || ||||||||||||||||| || ||     |||
----------------------------gtatacagttagttactttcgtgtgttgtgcaaaatattatttgttacaacggccttagagagttgctgactgagttcttcactc---cagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ17479 (Selaginella moellendorffii), 3'ss of exon 2
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                               |  |   | | ||  | |||        | ||   |     ||  |          |  |     ||   |||| ||||| || |  ||  ||||   |||  | ||||||||||| || || |||||||| || |||||||||||||| ||||| |||||||||  ||| |
----------------------------------------------gttggtgccatccatttaaacgcttacggctggttctctttaatgtttttttcttcttctttggactgtctagGATTTCCATTTTAAAGAGCTGGAGGAAGTGAGGAAATACTATCCACAGGGCCACCATGGAGTGGACAAAGAAGGAAGGCCTGTATATATTGAGAGGATCG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ21359 (Selaginella moellendorffii), 3'ss of exon 2
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaat---ttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                                              | ||  | || |    | ||   ||   |  |||| |        |  | |  || |||||| ||| ||||    ||  | ||   |||   |||||||||||||||||| |||||||| |||||||||||||| || ||  |||| || ||||   | |
-------------------------------------------------------------gtaaatgatatctcattgtatatctttttgtcactgtgaggaaaacttcgtttgtgtacagGATTTCGAGTTTGGTGAGATCGAGGAAGTGAAAAAATACTATCCTCAAGGTCACCATGGGGTTGACAAAGAAGGGAGGCCCATTTACATCGAGCGCTTGG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23906 (Selaginella moellendorffii), 3'ss of exon 2
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaat---ttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                                              | ||  | || |    | ||   ||   | ||||| |        |  | |  || |||||| ||| ||||    ||  | ||   |||   |||||||||||||||||| |||||||| |||||||||||||| || ||  |||| || ||||   | |
-------------------------------------------------------------gtaaatgatatctcattgtatatctttttgttactgtgaggaaaacttcgtttgtgtacagGATTTCGAGTTTGGTGAGATCGAGGAAGTGAAAAAATACTATCCTCAAGGTCACCATGGGGTTGACAAAGAAGGGAGGCCCATTTACATCGAGCGCTTGG

upper sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ28804 (Selaginella moellendorffii), 3'ss of exon 2
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
                                               |  |   | | ||  | ||         | ||   |     ||  |  |       |  |     ||   |||| ||||| ||||  ||  ||||   |||  | ||||||||||| ||||| |||||||| || |||||||||||||| ||||| |||||||||  ||| |
----------------------------------------------gtcggtgccatccatttaaaagcttacggctggttctctttaatgttttgttcttcttctttggactgtctagGATTTCCATTTCAAAGAGCTGGAGGAAGTGAGGAAATACTATCCACAAGGCCACCATGGAGTGGACAAAGAAGGAAGGCCTGTATATATTGAGAGGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG
     aatttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT