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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAATCACATAAACGGATTGGAGCTTGTATGCCGTGCGCATCAATTAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatataccattttttttttctgcccattattgttctatgattgaattgttcgagctgagctgattggaatatagccgttcaagagatatcttctacaag...

Basic information

species Physcomitrella patens
transcript PP1S207_36V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ05314 (Selaginella moellendorffii), 5'ss of exon 8
TTCAATCACATAAACGGATTGGAGCTTGTATGCCGTGCGCATCAATTAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatataccattttttttttctgcccattattgttctatgattgaattgttcgagctgagctgattggaatatagccgttcaagagatatcttctacaag
|| |||||||| || ||  ||||||| || ||||| || |||||| |||| || ||||||||||||||||||||||| || ||| | ||||||||||||   || |  || | ||   | | |   | | | |    || | |||   | |  ||     |  |                                
TTTAATCACATCAATGGTCTGGAGCTGGTGTGCCGAGCACATCAACTAGTACAGGAGGGATTGAAGTACATGTTTCCAGATAAAAGCCTTGTCACGgta---acaaagttctgttctagacgagactagctttc---ttaacttgcgggtgtcgaaaccttcag--------------------------------

upper sequence: PP1S207_36V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: EFJ25636 (Selaginella moellendorffii), 5'ss of exon 8
TTCAATCACATAAACGGATTGGAGCTTGTATGCCGTGCGCATCAATTAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatataccattttttttttctgcccattattgttctatgattgaattgttcgagctgagctgattggaatatagccgttcaagagatatcttctacaag
|| |||||||| || ||  ||||||| || ||||| || |||||| |||| || ||||||||||||||||||||||| || ||| | ||||||||||||   || |  || | ||   | | |   | | | |    || | |||   | |  ||     |  |                                
TTTAATCACATCAATGGTCTGGAGCTGGTGTGCCGAGCACATCAACTAGTACAGGAGGGATTGAAGTACATGTTTCCAGATAAAAGCCTTGTCACGgta---acaaagttctcttctagacgagactagctttc---ttaacttgcgggtgtcgaaaccttcag--------------------------------
















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|18338827|gb|BJ170852.1|BJ170852
EST:     TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
EST: gi|18334335|gb|BJ166352.1|BJ166352
EST:     TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
EST: gi|208366403|gb|DC947585.1|DC947585
EST:     TAGTTCAAGAGGGATTGAAGTACATG-TTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
EST: gi|100381804|gb|BY950182.1|BY950182
EST:     GTTTCA-GAGGGATTGAAGTACATGTTTCCCTGACAANG-ACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGC
genomic: GTT-CAAGAGGGATTGAAGTACATGTTTCC-TGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGC
EST: gi|208358797|gb|DC957625.1|DC957625
EST:     TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
EST: gi|208362791|gb|DC950591.1|DC950591
EST:     TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
EST: gi|37829309|gb|BJ587321.1|BJ587321
EST:     TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
EST: gi|37821893|gb|BJ579959.1|BJ579959
EST:     AAGTACATGTTTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: AAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
EST: gi|162174229|gb|FC350612.1|FC350612
EST:     TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACG                         GTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC
genomic: TAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatatacca ... tctgtttcagGTGTGGTCCGCTCCAAACTATTGCTACAGATGTGGAAATGTTGCTTCAATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAATCACATAAACGGATTGGAGCTTGTATGCCGTGCGCATCAATTAGTTCAAGAGGGATTGAAGTACATGTTTCCTGACAAAGGACTTGTCACGgtatataccattttttttttctgcccattattgttctatgattgaattgttcgagctgagctgattggaatatagccgttcaagagatatcttctacaag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG