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'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

Basic information

species Physcomitrella patens
transcript PP1S425_2V6.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
         || | |    | |  | |||    || |  | | |   |||||        |   | |  | |  |     ||| || | | |||| ||||||||||||||| ||||| || |||||||| || || || ||||| |||||| | ||||| |||||  | ||||| |||||||| || |||||
------gtgaagttt---cgtaacctgaatgatggcaaaaat-gtcaatgttaagacatgtcacaatctaatgccgtg--ttaatttcatctttt-gcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttt--tttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                      |  |||    |  ||     ||  ||       | | | || ||       ||| ||  ||  |    | |  ||| ||| | |||||||| ||||||||||| ||||| || || || |||||||||||| | ||||| |||||  | | ||| ||||||||||| ||  |
----------------------gtgagactttgtcaaccgaatgactaaaaagaagccatatg-atgactgatacataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgt--ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                  ||||       ||   |||| | ||    | |    | |    || |   || | |   || ||  | |  |   |  || |||||||||||||| || ||||| || ||||| ||||| ||||||||||| ||| | ||||| |||||  | ||||| ||||||||||| ||  |
-----------------gtgaaattctctcaactgaat-aattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgc-agCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                  |||     ||   |    || | ||  ||     ||| | || ||  ||  |       |   |  ||   |     ||| |||| |||||| | ||||| || |||||||||||||||||||| || |||||| | ||||| |||||  |||| |||||||||||||| |||||
---------------gtttgataagtgat--gaattatgaatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgccagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaatta-cttacgtttttttg--cagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
            || |     | |   |     | ||| ||     |   ||  ||  | || |||  |  ||| || || |  || |  ||||||||  ||||| |||||| | ||||| || |||||||| || |||||||||||||||||| | ||||| |||||  |||||||  |||||||||| |||||
----------gttagattcccatgtttatataagtaatgagcaa--tgaattcctgctgctt-tatcaag-tcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttg-gttatg--tttgtgtcgtttgtattgaactcacagaaattacttacgtttttttg--cagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                      |  |||         || | || |  |||  ||| ||  | || |||  |  |     || |  ||    ||||||||  ||||| |||||| | ||||| || |||||||| || |||||||||||||||||| | ||||| |||||  |||||||  ||||||| || |||||
----------------------gttagattcccatgtttggatgagcaatgaatttctgctgctt-tatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaat-tagttggttatgtttgtgtcgtttgtattgaa--ctcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                      |  ||| |       | | |    || | |||||    | ||| |||||  || ||     |   ||        |||||||| || ||||| ||||| || || || ||||| ||||| |||||||||||| | |||||||||||  || | |||||||| ||||| |||||
----------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattac--ttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                   |   |      |      | ||   | ||  ||||    ||| ||  |   || |  |  ||| |  ||  | |  ||| |||||||||||| | ||||| || ||||| ||||| || ||||| ||||||||| | |||||| ||||| |||| | ||| || ||||| |||||
-------------------gtcagtttcctaatattttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
  | |       |    | |||            |||  | ||   ||  ||  | || |   |  | |  | ||      |   |    || | | ||| | |||||| | ||||| || ||||||||||| ||||| ||||| |||||| | ||||| ||||| ||||||||||| || ||||| |||||
-gtgagcttgctttcctcagaaaagtcttacacagaacaactt--ctacattactctc-tgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
----------cttcaatcaaaatata---actgaaggcagaacaggggaattagttggtta---tgtttgtgtcgtttg---tattgaactcacagaaattac-ttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
          ||||  |  |||| ||    || |||||  || | |  |  ||  |  ||    |   ||| || |||     ||     |    | | ||    |  | | ||   ||| | || ||| | ||||| || ||||||||||| || ||||||||||||||| | ||||| ||||| |  || || ||||||||||| |||||
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------cttcaatcaaaatataactgaaggcagaacaggggaattagttgg---ttatgtttgtgtcgtttgtattg--aactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                        | |  |     |    ||       |||  | |  |||  ||||   ||||  |    |  | || | |    | | |     |||| |||  | ||  | ||||| |||||| | ||||| || ||||| |||||||| || |||||||||||| | ||||| |||||  | || || || ||||||||||||||
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttatt--ttgggctttattgtcaaataatatgaactatttaattattatcattatttaaatcttgat-cagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgttttt---ttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                                        ||||  | | |   ||||||| |  | |   |||| ||  || ||     ||||   |||||| | |||||  | ||||||||||||||  | ||||| || || ||||| ||||| |||||||||||| | ||||||||||| || ||||||||
----------------------------------------gttgcgtctttcgatgtcgttcgggtgg---tcactgactttgctggttcttttgcgttgcagTTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                                        ||||  | | |   ||||||| |  | |  |             ||   ||   |||||| | |||||  | ||||||||||||||  | ||||| || || ||||| ||||| |||||||||||| | ||||||||||| || ||||||||
----------------------------------------gttgcgtctttcgatgtcgttcgggtggtccctgactttgcgggttcttttgcgttgcagTTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAG

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|162255329|gb|FC432055.1|FC432055
EST:     AATCTGCTCCTGTGGCTACATTTAAAGTTCACGAGCATTTGCGACCAAAG                         CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT
genomic: AATCTGCTCCTGTGGCTACATTTAAAGTTCACGAGCATTTGCGACCAAAGgtgaaccttg ... ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT
EST: gi|162150294|gb|FC326379.1|FC326379
EST:     AATCTGCTCCTGTGGCTACATTTAAAGTTCACGAGCATTTGCGACCAAAG                         CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT
genomic: AATCTGCTCCTGTGGCTACATTTAAAGTTCACGAGCATTTGCGACCAAAGgtgaaccttg ... ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT
EST: gi|162258030|gb|FC434124.1|FC434124
EST:     AATCTGCTCCTGTGGCTACATTTAAAGTTCACGAGCATTTGCGACCAAAG                         CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT
genomic: AATCTGCTCCTGTGGCTACATTTAAAGTTCACGAGCATTTGCGACCAAAGgtgaaccttg ... ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                                    tacttac  putative branch site (score: 1)
                                          cgttttttt  CT-rich tract
                                aaattactta  TA-rich tract