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

GCTGTGAGGCGACGTTTTGACAAGCGTATCTACATCCCTCTACCCGAGTTTAAGGCTCGGCAGCACATGTTTAAGgtgctcatggtgttcaatattgcactcaactttcaagtgttcacgactaaatttactagacctattctaaatgttgtatgcttcaaatcaagtcgtttaacaatgacatgatcccccgtgaggtcttcacctccgtctcctcctgctactgtctcagcctttgttttcttgtccttgtgtag

Basic information

species Physcomitrella patens
transcript PP1S200_72V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S200_72V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os02g06490.1 (Oryza sativa), 5'ss of exon 5
GCTGTGAGGCGACGTTTTGACAAGCGTATCTACATCCCTCTACCCGAGTTTAAGGCTCGGCAGCACATGTTTAAGgtgctcatggtgttcaatattgcactcaactttcaagtgttcacgactaaatttactagacctattctaaatgttgtatgcttcaaatcaagtcgtttaacaatgacatgatcccccgt--gaggtcttcacctccgtctcctcctgctactgtctcagcctttgttttcttgtccttgtgtag
|||||  |||| ||||||||||| ||||||||||| || ||||||||  |||| ||| ||||||||||||| |||||         || |||                 |   |||  | |  | |   |  |||  |  ||| ||   || |  ||| |||   |  | ||| | || | | ||| ||    |  ||  ||  ||   | |                                               
GCTGTACGGCGGCGTTTTGACAAACGTATCTACATTCCGCTACCCGACCTTAAAGCTAGGCAGCACATGTTCAAGgtaa-------gtacaa-----------------agaagttagcaaaaagagcaatgagattt--tctcaaacatgcaaccttgaaactgaaacttttgataa-gtcttgaacctgaatctgaaatccgcattgcag-----------------------------------------------

upper sequence: PP1S200_72V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G088834_T01 (Zea mays), 5'ss of exon 5
GCTGTGAGGCGACGTTTTGACAAGCGTATCTACATCCCTCTACCCGAGTTTAAGGCTCGGCAGCACATGTTTAAGgtgctcatggtgttcaatattgcactcaactttcaagtgttcacgactaaatttactagacctattctaaatgttgtatgcttcaaatcaagtcgtttaacaatgacatgatcccccgtgaggtcttcacctccgtctcctcctgctactgtctcagcctttgttttcttgtccttgtgtag
|||||| ||||| | |||||||||||||||||||| || ||||| || || || ||  |||| ||||||||||||||   |||       ||  |||  ||     ||| |  ||| ||     |||  | | |       ||||   ||| |  | |||| |||    |                                                                                       
GCTGTGCGGCGAAGATTTGACAAGCGTATCTACATTCCGCTACCTGACTTGAAAGCAAGGCAACACATGTTTAAGgttaacataac---taagtttgtcctg----ttccatggtttac-----aatccattgg-------ctaacatttggaaccatcaattcatacag---------------------------------------------------------------------------------------

upper sequence: PP1S200_72V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 5'ss of exon 5
GCTGTGAGGCGACGTTTTGACAAGCGTATCTACATCCCTCTACCCGAGTTTAAGGCTCGGCAGCACATGTTTAAGgtgctcatggtgttcaatattgcactcaactttcaagtgttcacgactaaatttactagacctattctaaatgttgtatgcttcaaatcaagtcgtttaacaatgacatgatcccccgtgaggtcttcacctccgtctcctcctgctactgtctcagcctttgttttcttgtccttgtgtag
||| |  ||||||||||||||||||||||||| || ||||| || |||   |||||||||||||||||||| || ||  |  |  | | |   |     ||||| |   ||   |||| |    |    || ||     |  | |    ||| |  |  ||||  ||                                                                                          
GCTATCCGGCGACGTTTTGACAAGCGTATCTATATTCCTCTCCCAGAGGCCAAGGCTCGGCAGCACATGTTCAAAgtattattcatttgcttcaagtttctcaagtaaaaatcattcaagggagacagaaccagtttactaatgagatctgttt--tgtaaatgcag------------------------------------------------------------------------------------------

upper sequence: PP1S200_72V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 5'ss of exon 5
GCTGTGAGGCGACGTTTTGACAAGCGTATCTACATCCCTCTACCCGAGTTTAAGGCTCGGCAGCACATGTTTAAGgtgctcatggtgttcaatattgcactcaactttcaagtgttcacgactaaatttacta-gacctattctaaatgttgtatgcttcaaatcaagtcgtttaacaatgacatgatcccccgtgaggtcttcacctccgtctcctcctgctactgtctcagcctttgttttcttgtccttgtgtag
||  |  | || || ||||||||||| |||||||| ||||| || || || || ||  |||||||||||||||||||  |   ||  || | || |||| ||  |||  |       |  | ||| || |  | ||| || |     |||  |||| |    |     |  ||  |||   |||| ||      |||    ||  | |  |  || |  ||    ||| |                            
GCCATCCGACGGCGATTTGACAAGCGAATCTACATTCCTCTTCCAGATTTGAAAGCAAGGCAGCACATGTTTAAGgtaatg--ggattttattaatgcattcttcttagacaaccagagcaataatttcatcatgacatagttc---tgtattatgtt----actgtatgtttctacag-aacattatttgtt-tgaccggttgccttatggatcttgatggctatgtgtag--------------------------

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|162277252|gb|FC453682.1|FC453682
EST:     GTATCTACATCCCTCTACCCGAGTTTAAGGCTCGGCAGCACATGTTTAAG                         GTTCATTTGGGAGATACACCAAACAACTTGACTGAACGCGATTATGAGGAT
genomic: GTATCTACATCCCTCTACCCGAGTTTAAGGCTCGGCAGCACATGTTTAAGgtgctcatgg ... ccttgtgtagGTTCATTTGGGAGATACACCAAACAACTTGACTGAACGCGATTATGAGGAT