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'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcttcaaaagtatttgtaaataatgtctcttaattccatgctttagaatctcacgtcactgatgtcgatgcttacgatattgtgtttggttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTTGAAAAACCTTGACGTTGAGATGATCCAACAGTCGTACACTGTGTAGAAG

Basic information

species Physcomitrella patens
transcript PP1S6_11V6.1
intron # 17
splice site 3'
intron type U2

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|162198176|gb|FC375479.1|FC375479
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162267611|gb|FC444674.1|FC444674
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162164470|gb|FC341583.1|FC341583
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162167183|gb|FC342748.1|FC342748
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162163563|gb|FC339473.1|FC339473
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162198820|gb|FC374303.1|FC374303
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162185477|gb|FC362559.1|FC362559
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162168957|gb|FC345639.1|FC345639
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162198373|gb|FC375546.1|FC375546
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162167182|gb|FC342747.1|FC342747
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162259297|gb|FC435681.1|FC435681
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162193950|gb|FC371763.1|FC371763
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162252634|gb|FC428665.1|FC428665
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162164471|gb|FC341584.1|FC341584
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162185797|gb|FC362353.1|FC362353
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162157210|gb|FC332844.1|FC332844
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162184821|gb|FC361123.1|FC361123
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162252826|gb|FC428857.1|FC428857
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162183361|gb|FC359276.1|FC359276
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162156918|gb|FC333072.1|FC333072
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162159441|gb|FC336230.1|FC336230
EST:     GAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162174467|gb|FC350746.1|FC350746
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|162156917|gb|FC333071.1|FC333071
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
EST: gi|37845329|gb|BJ603337.1|BJ603337
EST:     GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAG                         GCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT
genomic: GAGCTTGGATTCATGGCTGAGCAGGCCAAGAGGAGGGCTGAGATTGCAAGgtacacatca ... gttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatctcacgtcactgatgtcgatgcttacgatattgtgtttggttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTTGAAAAACCTTGACGTTGAGATGATCCAACAGTCGTACACTGTGTAGAAG
                         tgcttac  putative branch site (score: 2)
                                 atattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttcaaaagtatttgtaaataatgtctcttaattccatgctttagaatctcacgtcactgatgtcgatgcttacgatattgtgtttggttgctacagGCTACGGGAGTTGAACACTCTCAAGGGACATGTAGAATCTGTTGTTCGCTTGAAAAACCTTGACGTTGAGATGATCCAACAGTCGTACACTGTGTAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG