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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATTTGATGAGATGGGTCAAGTTGTGGGAGTCACCTCTGAGGGTGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttgtgatttgaaagttgttgctagcagtctatcgtgaacttgtagagaatagtaggcttacacatggtatgggttgacttatgcgatgcataaaaccacctgctcctccag

Basic information

species Physcomitrella patens
transcript PP1S100_23V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 9
TGAATTTGATGAGATGGGTCAAGTTGTGGGAGTCACCTCTGAGGGTGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttgtgatttgaaagttgttgctagcagt--ctatcgtgaacttgtagagaatagtaggcttacacatggtatgggttgacttatgcgatgcataaaaccacctgctcctccag---------------------------------------------------------------------
||||||||||  |   ||  ||||    || || || || || || || || |  ||   |||||||||||||||||||||||| || || ||||| ||||| | |||| |    || |    |         ||   | |  |    |  |   | ||| |    |  || ||   ||     ||  |   | ||  |    ||    |  | || | |                                                                     
TGAATTTGATATGGAAGGGAAAGTCTGCGGCGTTACATCAGAAGGAGAAACTGCAAAATGCAAGAAAGTTGTTTGTGACCCTTCCTACTTACCCAACAAGgttaattttctttcctgtattcagcacaggattgttcttttaatatgttcttctgggatatttaaatgtcatattccatctcaagatattcacaattgaacttactgtgtttttcttctgcccttccatttgttgataagttttattaactgcaacctcatttgatgttctgcttacgtttattaacag

upper sequence: PP1S100_23V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 5'ss of exon 9
TGAATTTGATGAGATGGGTCAAGTTGTGGGAGTCACCTCTGAGGGTGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttgtgatttgaaagttgttgctagcagtctatcgtgaacttgtagagaatagtaggcttacacatggtatgggttgacttatgcgatgcataaaaccacctgctcctccag
 || |||||||||   ||  ||| ||| || || || || || || || || |  | |  |||||||||||| ||||| ||||| ||||||||||| |||||||||| | ||| |      |||||| ||  | || || | |  ||| ||| | |||       ||    || | |  ||| ||  ||   ||   ||| |                
AGAGTTTGATGAGGAAGGAAAAGCTGTTGGTGTTACATCAGAAGGGGAAACTGCTAGGTGCAAGAAAGTTGTCTGTGATCCTTCCTATTTGCCCAACAAGgtaatttgtttgaat---gccttgttgatattattccatagcgg-cttttag-gcatacacaatataagtctgcttttagtt-acccattttatttgtaagagatt------------
















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|37840302|gb|BJ598310.1|BJ598310
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAG                         GTTAAGAAGGTCGGGAAGGTTGT--GCGCTATCTGCTTCATGAGCCATCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttg ... gctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
EST: gi|67698955|gb|BJ959188.1|BJ959188
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAG                         GTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttg ... gctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
EST: gi|162225722|gb|FC401864.1|FC401864
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAG                         GTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttg ... gctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
EST: gi|18335062|gb|BJ167080.1|BJ167080
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAG                         GTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttg ... gctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
EST: gi|162225721|gb|FC401863.1|FC401863
EST:     CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCNCAATAAG                         GTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
genomic: CCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttg ... gctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
EST: gi|37847853|gb|BJ605861.1|BJ605861
EST:     TGCCCAATAAG                         GTTAAGAAGGTCGGGAAGGTTGT--GCGCTATCTGCTTCATGAGCCATCCA
genomic: TGCCCAATAAGgtaatttttg ... gctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
EST: gi|162159100|gb|FC334271.1|FC334271
EST:     GGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAG                         GTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA
genomic: GGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttg ... gctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATTTGATGAGATGGGTCAAGTTGTGGGAGTCACCTCTGAGGGTGAGACCGTGAAGGCCAAGAAAGTTGTTTGTGACCCTTCATATTTGCCCAATAAGgtaatttttgtgatttgaaagttgttgctagcagtctatcgtgaacttgtagagaatagtaggcttacacatggtatgggttgacttatgcgatgcataaaaccacctgctcctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA