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

GAAGCCCTTGCCTATGCTGAAAGTAACGGCATGTTCTTCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattcacacatcacttgggtttaattgtcagtgttgcagtccttcatttggcatgcattgaagtgtattatggttgagtgggatttagattcacct...

Basic information

species Physcomitrella patens
transcript PP1S543_3V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S543_3V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 7
GAAGCCCTTGCCTATGCTGAAAGTAACGGCATGTTCTTCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattcacacatcacttgggtttaattgtcagtgttgcagtccttcatttggcatgc--attgaagtgtattatggttgagtgggatttagattcacct-
||||| |  |  ||||| || |  ||    ||| | |||||||| || ||||||||||| ||||||||| | || ||| ||||||||||  |   | |  | ||  ||    || |||             |    |   ||   ||  |    ||   ||  |  || | |   | ||| ||  | || 
GAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAGgtatg--ccccctagcatatgaagctatttgctttcacgatgtccaagaagcaggatagctaacaagagaacatgctattttatttcaaatta-atcaagctg

upper sequence: PP1S543_3V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 7
GAAGCCCTTGCCTATGCTGAAAGTAACGGCATGTTCTTCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgag-attcacacatcacttgggtttaattgtcagtgttgcagtcc------ttcatttggcatgcattgaagtgtattatggttgagtgggatttagattcacct
|| |   | |    ||| || |  ||||||||||||||||| || |||||||| ||||| || |||||  | |||||| | ||||||||| | | |      |  | |  | || ||  ||  | ||   ||||      || |||  |     |||      |  | |  |||  | ||| || ||       
GATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAGgtgtgcacttctttcttgcctctgatttatgatcgattttcttgtcctctgcatttattgagatcttattatccgtttctttcattgctttggaattgga-------
















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|208344998|gb|DC925408.1|DC925408
EST:     TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAG                         -A--TTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
genomic: TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattca ... attttgacagGAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
EST: gi|37837038|gb|BJ595046.1|BJ595046
EST:     TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAG                         GAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
genomic: TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattca ... attttgacagGAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
EST: gi|67721680|gb|BJ971939.1|BJ971939
EST:     TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCGATTATTTGAG                         GAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
genomic: TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattca ... attttgacagGAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
EST: gi|37831837|gb|BJ589849.1|BJ589849
EST:     TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAG                         GAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
genomic: TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattca ... attttgacagGAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
EST: gi|208374825|gb|DC956098.1|DC956098
EST:     TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAG                         GAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA
genomic: TCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattca ... attttgacagGAGATTGCCAAGAGGTTACCTCGGGGACAATCAAGCTTGTCAAGGAATTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCCCTTGCCTATGCTGAAAGTAACGGCATGTTCTTCATCGAAACGTCAGCAAAGACTGCTGATAATGTGAATCAATTATTTGAGgtgagattcacacatcacttgggtttaattgtcagtgttgcagtccttcatttggcatgcattgaagtgtattatggttgagtgggatttagattcacct

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT