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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcctcgtaaaatataacctgatcactttttccggcactttgctttctatcctatcagtcataagtatgtcctaacctggtgaacccttggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACTGCATGATATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGT

Basic information

species Physcomitrella patens
transcript PP1S64_28V6.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S64_28V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G103070_T01 (Zea mays), 3'ss of exon 14
catcctcgtaaaatataacct-gatcactttttccggcactttgctttctatcctat-cagtcataagtatgtcctaacctggtgaacccttggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACTGCATGATATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGT
            || | | || |||    |          || ||||    | | |    ||  |    ||  |||    |||   | | |||      ||| || |||   || || || ||    || ||  ||||||| || || ||||| ||||||||||||||||| || || ||||| |||||||| ||| | || 
----------gtatgtgatctagattgtatccaatcctggttcgcttcagcttcgaagtggttgttgaaatagcct---ttggatgatcattg------cagTTCCAGAGAGAGGTCAGAACAGTCTCTTGTTAGATGGGCTACCCCTCAACTTCATGATATTGATGCACTTGCTAGGATGGTTGATCCAGCATTAAACGGA

upper sequence: PP1S64_28V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 14
----------catcctcgtaaaatataacctgatcactttttccggcactttgc---tttctatcctat-cagtcataagtatgtcctaacctg---gtgaacccttggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACTGCATGATATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGT
            |  || | |  | |   || |    |||   |   | | |||   |||  |   ||| ||   ||||  ||||  |  ||||   |  || | ||  |    ||||||||| |||||||| |||||     |||| |||||||||||||| ||||| ||||||||||||||| | || | |||||| ||||| ||  |  | || 
gtgaattaatggttttctttatgtctgctctcacgtttttgagcaatattctgcagattttgaaattatgcacaaataataatgttgtctcctgattgcaaaacattccatg-acagCTCAAGGCCAAGATCTGAGCAGTCTTTGGTTCGATGGGCAACACCTCAACTCCATGATATTGATGCATTGGCTAAAATGGTTGATCCTGCAATGAAAGGG

upper sequence: PP1S64_28V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA03G42360.1 (Glycine max), 3'ss of exon 16
-----------catcctcgtaaaatataacctgatcactttttccggcactttgctt---tctatcctat-cagtcataagtatgtcctaacctggt---gaacccttggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACTGCATGATATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGT
             |  |  |    | |   || |    |||   |   | | |||     |  |   |||  ||  ||||  ||||  |  |||| |   ||| | ||       ||||||||| |||||||| |||||     |||| |||||||||||||| ||||| ||||||||||||||| | || | |||||| ||||| ||  |  | || 
gtgaattaatggttttttttttggtctgctctcacgtttttgagcaatattctgcagaaattgaaattatgtagatataataatgttgtctcctgattgcgaaacattctgta-acagCTCAAGGCCAAGATCTGAGCAGTCTTTGGTTCGATGGGCAACACCTCAACTCCATGATATTGATGCATTGGCTAAAATGGTTGATCCTGCAATGAAAGGG

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|162151051|gb|FC326868.1|FC326868
EST:     TTTGGTGTTGTGATGCTTGAGCTTATGACAGGACGCAAGCCTTTAGACAG                         CTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACT
genomic: TTTGGTGTTGTGATGCTTGAGCTTATGACAGGACGCAAGCCTTTAGACAGgtaactcgaa ... ggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACT
EST: gi|162155001|gb|FC331419.1|FC331419
EST:     TTTGGTGTTGTGATGCTTGAGCTTATGACAGGACGCAAGCCTTTAGACAG                         CTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACT
genomic: TTTGGTGTTGTGATGCTTGAGCTTATGACAGGACGCAAGCCTTTAGACAGgtaactcgaa ... ggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatcctatcagtcataagtatgtcctaacctggtgaacccttggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACTGCATGATATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGT
                         tcctaac  putative branch site (score: 1)
                ataagtat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcctcgtaaaatataacctgatcactttttccggcactttgctttctatcctatcagtcataagtatgtcctaacctggtgaacccttggacccgcagCTCAAGACCAAGATCCGAGCAAAACCTGGTGCGATGGGCAACACCACAACTGCATGATATTGATGCACTCGCAAGAATGGTGGATCCAGCGTTAGAGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA