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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattggagttgggtttttgttgggcgcaagaatttttggaatttgggggagaagtgttgggacctctgtattagggtttaggggtttgcatgctgtgtttttttggggagctgagagtgaagttgtggtctctgcagCCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCGTATCCTT

Basic information

species Physcomitrella patens
transcript PP1S371_31V6.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 2
gtgagattggagttgggtttttgttgggcgcaagaatttttggaatttgggggagaagtgttgggacctctgtattagggttt-aggggtttgcatgctgtgttt---ttttggggagctgagagtgaagttgtggtctctgcagCCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCGTATCCTT
                                                              |  |     ||   || |    ||| |||| || |    ||     |||||  |  || |   | |  |     | | |||||  || |||||||||||  | || |||||| |  | |||| |||||||||||||||||||||||| || |||||||| ||||||||| | ||         
--------------------------------------------------------------gtaagtcaagttcaagagaccgaggcgtttccaagtcaagtcaaggttttgacgtacttaatctcatttgtcattgtttgcagAGGGCAAGACTGACTACAGGGCCAGGATTAGGCTCACCAACCAAGATAAGAACAAGTACAACACACCGAAGTACCGCTTCGTTGTGAGATTT--------

upper sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 2
gtgagattggagttgggtttttgttgggcgcaagaatttttggaatttgggggagaagtgttgggacctctgtattagggtttaggggtttgca-tgctgtgtttttttggggagctgagagtgaagttgtggtctctgcagCCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCGTATCCTT
                                         | || ||       |    ||    | | ||  | | |  ||  | | ||| | |   |     |||||  |  || |   | |  |  |  | | |||||  || |||||||||||  | || |||||| |  | |||| |||||||||||||||||||||||| || |||||||| ||||||                 
-----------------------------------------gtaagttcaatataatccttt----catgtggctcatgcattctgtgcttgtaatatagctaggttttgatgtacttaatctcatttgttattgtttgcagAGGGCAAGACTGACTACAGGGCCAGGATTAGGCTCACCAACCAAGATAAGAACAAGTACAACACACCGAAGTACCGCTTCGTT-----------------

upper sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgagattggagttgggtttttgttgggcgcaagaatttttggaatttgggggagaagtgttgggacctctgtattagggtt-taggggtttgcatgctgtgtttttttggggagctgagagtgaagttgtggtctctgcagCCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCGTATCCTT
         |  |||   | |||||     ||||      | || || |         | || || |   | |||   | || || ||| ||   || ||||   |    |  || ||    ||   || |  |||  | ||  ||||||||||| ||  | || ||||| ||  | | ||  ||||| |||||||||||||||||||| ||||||||||| ||||| || ||      |  
---------gtattgatctgttgttactgtcaag-----ctagacttcgc--------tttttggtctgttatatagagtttatatgggattaggtgttgtgacct----gaaagttgt---tgttcttataatct--gtagATGGGAAGACTGATTACAGGGCAAGGATCCGTCTTATCAATCAAGACAAGAACAAGTACAACACCCCTAAGTACCGTTTTGTTGTTCGATTTACCAACAA

upper sequence: PP1S371_31V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 3
gtgagattggagttgggtttttgttgggcgcaagaatttttggaatttgggggagaagtgttgggacctctgtattagggtttaggggtttgcatgctgtgtttttttggggagctgagagtgaagttgtggtctctgcagCCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCGTATCCTT
                           |   | | |||  |            |  | ||| |   ||||  | |   |||||   |||| ||    | | ||||  ||| | |||        | |||       || ||| || ||||| ||||||||||| ||||||||| ||| ||  ||||| ||||| ||||||||||| || || || || || || ||||| ||         
---------------------------gtata-gtattcctcttgccccttcaaatattgtggtagcctcctttt---ggttt---ggttagc----tctattttgatggtgtgct--------atttgcaaatcgtgtagCGGGCAAGACAGACTATCGTGCCAGGATTCGCCTGATCAATCAAGACAAGAATAAGTACAACACTCCAAAATATCGATTTGTCGTGCGATTT--------

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|18368062|gb|BJ200147.1|BJ200147
EST:     GACTAAGGCTTACTTCAAGAGGTTTCAAGTCAAGTACAAACGCCGGAGAG                         CCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGA
genomic: GACTAAGGCTTACTTCAAGAGGTTTCAAGTCAAGTACAAACGCCGGAGAGgtgagattgg ... gtctctgcagCCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttgcatgctgtgtttttttggggagctgagagtgaagttgtggtctctgcagCCGGGAAGACTGACTATCGTGCGAGGATTCGCTTGACCACCCAAGATAAGAACAAGTACAACACCCCCAAGTACCGTTTCGTTGTGCGGTTCGTATCCTT
                                              tctctgc  CT-rich tract
             tgttttttt  TA-rich tract