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

...gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcctacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGCCAGTCGGCTCCAAAG

Basic information

species Physcomitrella patens
transcript PP1S85_160V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 1
-------gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcctac-atagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGCCAG-TCGGCTCCAAAG
         | |         |||||  |||||      |   |    ||   | |         | || |   ||     ||   |      | |  |     | ||||| ||||||||||| ||||| ||||| ||||||||||| || || |  || || || || ||  |||| ||  ||||    ||||||  | |  ||||  
gtaagcctccctctctctctctctttccagatctgcgcgcggagagcgtgcgccgcggc------gaatctgaggcgggtgatgagaatgggtggcgcgcgcgcgcagGTACACGAAGATGGGGTTCGCCGGGAACGTGGAGCCCTGCTTCATCACCCCCACCGTCGTCGCCGTCAACGACACCTTCGCCGGCCAGACCAGGGCCAAC-

upper sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 1
gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcctacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGCCAGTCGGCTCCAAAG
         |  || |  |     ||   |||  ||      |  || | |   | |||        || | | |    | |  || |        | ||||| ||||||||||| ||||| ||||| ||||||||||| || || |  || || || || ||  |||| || ||||| |  |||    |    ||   |
---------gtacgcccctcccactccctagatctgcgcgcggaggcgcgac--ggcggtgagccacgc-tgc-tgatctgttccggctctcgcg-gcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTCTCCGGCTCCGCCCAGCCGGCG

upper sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G106513_T01 (Zea mays), 3'ss of exon 1
gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcctacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGC-CAGTCGGCTCCAAAG
         |  || |  |     ||   |||  ||    | |  || | |   |||||        || | | |    | |  || |        | ||||| ||||||||||| || || ||||||||||||||||| || || |  || || || || |   |||| || ||||| | |||| | | |   ||   | 
---------gtacgcccctccctctccctagatctgcgcgtggaggcgcgac--gacggtgagccacgc-tgc-tgatctgttccggctctcgcg-gcagGTACACGAAGATGGGGTTTGCGGGGAATGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGACGTCAACGATTCCTTCTCGGGCTCCGCCCAGTCGGCA-

upper sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 1
gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcc-tacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGC-CAGTCGGCTCCAAAG
        |   | ||  |     ||   |||  ||         || | |   |||||    |   ||     ||    ||  ||           | ||||| ||||||||||| ||||| ||||| ||||||||||| || || |  || || || || ||  |||| || |||||||  ||  ||| |    |     
------gtacgacctccctccctctccctagatctgcgcgcgaaggcgcgac--gacggtgagtcacgctgctgatctgctcctactctcgctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG-

upper sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ09569 (Selaginella moellendorffii), 3'ss of exon 1
gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcctacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGCCAGTCGGCTCCAAAG
     |||  |   ||  |  ||| ||     |    | ||  | |  | |||   | |   || ||   | |||     ||              | || ||  | ||||| ||||||||||||||||||||||| |  || || || || || || |||||  |||| |||||||   | | |   ||  ||||    
----gtaagaacgatcgatctagagcgctgcccgcattcttccttgtgcgatt---cagatcatcgaaatttcat----ccttg------------gcagCTACTCCAAGATTGGATTCGCAGGGAATGTGGAGCCGTCCTTCATAATCCCCACGGTCGTGGCGATCAACGAGTCCTGCCTCGCCGCTTCCTCTCCTGCC

upper sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ18143 (Selaginella moellendorffii), 3'ss of exon 1
gtctttaaagatcgtctttaaagatcgtgagacatggt--atttgtagctcaatttgacggcatattgagcctacatagaatctcacgacatgaatat--gtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGCCAGTCGGCTCCAAAG
                          || ||| | | |  || |  ||| |    ||    | |  |    | |   |||   ||   |  | |   |  | || ||  | ||||| ||||||||||||||||||||||| |  || || || || || || |||||  |||| |||||||   | | |   ||  ||||    
--------------------------gtaaga-acgatcgatctagagcgctgcctgcattcttccttctgcgattcagatcatcgaaatttcatccttggcagCTACTCCAAGATTGGATTCGCAGGGAATGTGGAGCCGTCCTTCATAATCCCCACGGTCGTGGCGATCAACGAGTCCTGCCTCGCCGCTTCCTCTCCTGCC

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|100404540|gb|BY973629.1|BY973629
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|18351206|gb|BJ183257.1|BJ183257
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100397452|gb|BY972506.1|BY972506
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTACTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|67570355|gb|BJ943179.1|BJ943179
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100448162|gb|CJ972461.1|CJ972461
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|208359135|gb|DC930467.1|DC930467
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100440187|gb|BY980439.1|BY980439
EST:     GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GAGATGGATGCTACTCAACGTCCTGCTGTTGTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
EST: gi|100365851|gb|BY967178.1|BY967178
EST:     GTCATCGACAATGGCACCGG                         GTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC
genomic: GTCATCGACAATGGCACCGGgtatgtttgt ... gaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcaatttgacggcatattgagcctacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGCCAGTCGGCTCCAAAG
                                 atctcac  putative branch site (score: 3)
                                           atgaatat  TA-rich tract