Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG

Basic information

species Physcomitrella patens
transcript PP1S147_62V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                || |  |   |    |   |   | |  || || ||| ||       |||      ||||| |  ||  | |  |  |  |  | |  |  | |    | ||   |  | |||||| || ||| | ||||| ||| |  ||||  |  ||||  | | ||| ||||||| ||| |||||||||||| | || ||||||||||||||||| || 
--------------------------------------------------------------------------------ttgcctattgagttttgcctt--acagtggctttaatattgtagtatatt------ttaca-actaattatgttactgtattcattgaacatat----gaaccaattttacagGTTTAAGTGTATTGACCTTGATGGAAATGGCATTTTAACCACCACTGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os02g09840.1 (Oryza sativa), 3'ss of exon 8
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                       ||||  | | |      |      |   | ||    |  | |||| | |||  |||         |||     ||| |||| |  |  |   ||  |    | |||||||| |||| | ||  ||||| |  ||||  |  | ||||  |||||  | || |  |||| |||||||||||||||||| ||||| |||||||| |||
---------------------------------------------------------------------------------------caaatgaatgtcacttctcttatttgtcacttcttttgagcttgagt-gttgaatattct----aacaatttatcttatttgtgctg-cacataatctctcttcagGTTCAGATGTATAGATGTGGATGGCAATGGCATTCTCACACATAATGAACTACAGTTCTTTTTTGAGGAGCAACTTCATCGCATGGAATGCATGGCCCAG

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G080083_T02 (Zea mays), 3'ss of exon 8
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                           |||   || |  |  ||    | || ||||          |  |      ||||| | |  |  ||   | |  ||| || ||  |   ||      | ||||||||||||| | ||  ||||  |  ||||  |  | ||||  | |||  | || |  || | |||||||||||||||||| |||||||||||||| |||
-----------------------------------------------------------------------------------------gtacaagcttca--actaaatcctaaaatttcttatcctccaaccaagcctgtaacatccaaaagttctcatat--ttttttcttggtgacaccatctcttcagGTTCAAATGTATAGATTTGGACGGCAATGGCATACTTACACATATTGAACTACAGTTCTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAG

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G040094_T01 (Zea mays), 3'ss of exon 8
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctga----tgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                           ||   ||      |||||| |   |||     |    |   |||    |||  |    |   ||     ||| ||  |||||| ||||   || | |    | |||||||| |||| | ||  ||||| |  ||||  |  | ||||  | ||| || ||||  ||||  ||||||||||||||||| |||||||||||||| || 
-------------------------------------------------------------------------------------------actaaatcc----taaaggttcatattgatcattccttatcttacaagcatgcctgtaacttcaaaagttctcat--atttttgcttggtgacatcacctcttcagGTTCACATGTATAGATTTGGATGGCAATGGCATACTTACACACATTGAAATACAATTCTTTTTCGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G104254_T01 (Zea mays), 3'ss of exon 5
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtac-acctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                         |  | ||||||    || |  |||| ||    |||| | |||  ||||| |||       |  | || |    |  ||  | ||    | |   |     |||||||| || ||  | || || ||| || ||||| |  ||||    ||||| ||||||| ||| |||||||||||| | || || |||||||||||||| |||
----------------------------------------------------------------------------------------tattctgtatttgttgtacat-attgtata---actcagcttg--tagttgcattttctttaaaatattgtaattgtttgttattgaaatatgttaaaatttgcagGTTTAAGTGCATCGATCTTGATGGTAATGGTATTTTAACTTACAATGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAG

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                          || |      ||  ||  ||||||||  |    | | |   | |||          |||| | | |||   ||     || || |     |||| |||||      | |  |  || |||||||||||  | ||  ||||| |  |||| ||| | ||||||||||| ||||| |  ||||||||||||||  | |||||||||||||||||||| || 
------------------------------------------------------------------------atatttctagattgtaaattcagtatttcagtagcaagttcagaattt----------gatttgctgcatt-taatagaaac-tcaac----atttgttttta-----aaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgat--gcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                           |   ||||| | | | ||     | ||  || |  | |||| | |||   | |     | | | || |    | |      |  |||| | |  | |     |||||||| ||  | ||  ||||| |  |||| ||  | |||   |||||  |||||| |||||||||||| ||| | |||||||||||||||||||| || 
-------------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacattgtggttgacttgttttctgatttttaagtcgtcaa----agtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAACTGCAATTTTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgat--gcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                           |   ||||| | | | ||     | ||  ||    | |||| | |||   |       | | |||| |    | |      |  |||| | |  | |     |||||||| ||  | ||  ||||| |  |||| ||  |||||   |||||  |||||| |||||||||||||||| | ||||||||||| |||||||| || 
-------------------------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaa----agtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatg--cagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                               | ||     |       | | |   | ||  |    |      |  |   | |   |   | || | | |  ||||| |  ||  ||   | |||   |||||||| ||  | ||  ||||| |  |||| ||  | ||||  |||||  |||||| |||||||||||||||| | ||||| |||||||||||||| || 
-----------------------------------------------------------------------------------------------ttttccaccttgcctcctaagtacactcttaggcgaacattggaagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgcttt-ctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                           |   | || |   | ||  |   | |  |   ||   | ||| ||| ||     | | ||   | | |   | | |               ||| |  |||  |||   | ||||  |||||||| ||  | ||  ||||| |  |||| ||  | ||||  |||||  |||||| |||||||||||||||| | ||||| |||||||||||||| || 
---------------------------------------------------------------------------tccaccttgcctcctaagtacactcttaggcgaacattggaagtttgacctttgt-ggttgact-cttgttagcta---------------tttgtgatttgatgtgt-catgat-tagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                          || |      ||  ||  |||||||| || ||    ||| |   ||         ||||| | | |||   ||     ||           |  |  |||||    | |  |  || |||||||||||  | ||  ||||| |  |||| ||| | ||||| ||||| ||||| |  ||||||||||||||  | |||||||||||||||||||| || 
-----------------------------------------------------------------------tatatttatagattgtaaattcagtattttgg-tagcaaattcagaatt---------tgatttgctgcatt-taatagaaac-----------tcaacattttcaaaaaaaaatcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCTAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgta-cacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                                                                         ||    ||  |  | |  |   ||   ||  ||   ||     | | |    | ||||||||||||| | || ||||||||||| || ||| | || ||||| |||||||| || ||||| ||||||||| | ||||| ||||||||| | ||||| 
----------------------------------------------------------------------------------------------------------------------------------------gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTACGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA

upper sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgta-cacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                                                                                                                                         ||    ||  |  | |  |   ||   ||  ||   ||     | | |    | ||||||||||||| | || ||||||||||| || ||| | || ||||| |||||||| || ||||||||||||||| | ||||| ||||||||| | ||||| 
----------------------------------------------------------------------------------------------------------------------------------------gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA

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|162193203|gb|FC369963.1|FC369963
EST:     TTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCTTAGAATACTG                         GTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGAT
genomic: TTCATTCTTTCAGAAGAGGACAAGTCTTCAGAACCTAGCTTAGAATACTGgtacgtacct ... cctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
                      tctaatttattttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA