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

...acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG

Basic information

species Physcomitrella patens
transcript PP1S83_83V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os03g56300.1 (Oryza sativa), 3'ss of exon 6
----acctgtcactaataccctcatttccactcgg-ttatctacagctg--tcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
     || ||  ||      ||    |||    |  ||||  | |  ||  |  ||   | |  |   |  |   ||||||    | ||     ||   |||||||||||||||||||| ||||| ||||||||||| || ||||| |||||||||||||| ||||| || || || || || |||||||||||||||||  | || 
gtaatcccgtggctggctttctttgatccgtgtgaattattgaaaaatgatttactgcctcttcatctgctgttaagctctgttgtgatg--aactcctttttgcagATATGATATTGATATGACCAAATGCATCTATTGTGGCTTCTGCCAAGAAGCTTGTCCTGTTGATGCCATCGTTGAGGGTCCTAACTTTGAGTTTGCTACT

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G072806_T01 (Zea mays), 3'ss of exon 6
--acctgtcactaataccctcatttccactcggttatctacagctgtcgcttg---atttagagtcgtaggcgagctctaa-----gtttattctgcctgtatt---ttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
  |      |  ||     |  | ||   |  || |  || | || |   ||    | |  |    | |    | || |||      ||| |  ||| | |||    |  ||| ||||||||||||||||| |||||||| ||||| || || |||||||| |||||||| || || |||||||| || || ||||||||||||||  | || 
gtaatcaaaatgaaggtttttctctcttttttgtcaa-tagaactatgatttacccactgtgttctgcaattaaactttaatctgaatttctgttgcttttatctcctcacagGTATGATATTGACATGACCAAATGCATTTACTGTGGGTTCTGCCAAGAGGCTTGCCCAGTCGATGCTATTGTTGAGGGGCCTAACTTTGAGTTTGCTACT

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AC195340.3_FGT002 (Zea mays), 3'ss of exon 6
------------------------------------acctgtcactaataccctcatttccactcgg--ttatctacagctg-tcg---------cttgatttagagtcgtaggcga---------gctctaagtttattctgcctgtattttg---cagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
                                    || |||  || ||| |    |||| |||||    || ||  |  || | |         |||  ||     || || || |           ||| |  || |  ||| | | | |     ||||||||||||||||||||| |||||||| ||||| || || || ||||| |||||||| || || |||||||| || || ||||||||||||||  |||| 
gtaatcaaaatgaagtttttcctctttcttttttggacttgtggctgatatcgg-gtttcaactcgagtctacctcaacttgattgggacaaagtctttgttgttgttcttatgcaattaaacttcattctgaacttgtgttgcttttttctcatcacagATATGATATTGACATGACCAAATGCATTTACTGTGGGTTCTGTCAAGAGGCTTGCCCAGTCGATGCTATTGTTGAGGGGCCTAACTTTGAGTTTGCCACT

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA05G34890.1 (Glycine max), 3'ss of exon 6
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
                      |  | |   ||   |       || | |  |   |   | ||  | |    ||   |||||     |  || || ||| ||||||||||||||||| || |||||||| || || ||||| ||||| || |||||||| || || ||||| ||||| || |||||||| ||  | || 
---------------------gtgaattaccttccttgtgtacctccccttctcctgcccc-tatcccattcttactgttatttg--ttaaatctttcagGTATGATATTGACATGACCAAGTGCATCTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCCATTGTTGAAGGGCCAAACTTTGAATTTGCTACA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G31520.1 (Glycine max), 3'ss of exon 7
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
                   ||| |||  |  |||||| |  |      ||  |        | |  |  |||||    ||||| ||    ||  |  ||| ||||||||||||||||| || |||||||| || || ||||| ||||| || |||||||| || || ||||| ||||| || |||||||| ||  | || 
---------------gtgaattaccagcc--ttatctgctccctcttttttttccctcactgcattcttgctct---cttatt-tgt---taaatctcagGTATGATATTGACATGACCAAGTGCATCTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCCATTGTCGAAGGACCAAACTTTGAATTTGCTACT

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttatt-ctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
                         | |    | |||  | ||| |   || |||     | |        ||||  | | ||  |   |  || || ||| ||||||||||||||||| || ||||| || || || ||||| ||||| || |||||||| || || ||||| ||||| || |||||||| ||  | || 
----------------------gtgaattacctgtct-tacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G16700.1 (Arabidopsis thaliana), 3'ss of exon 7
acctgtcactaataccctcatttccactcg-------gttatctacagctgtcgcttgatttagagtcgtaggcg-agctctaagtttatt--ctgcctgtattt-tgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
  |   | ||||   ||   ||   |  |         |||| ||   |||||   |   |  |  || |      |  ||  ||| || |   ||   | |  | | ||| |||||||| |||||||| ||||||||||| || || || |||||||||||||||||||| || || || |||||||| || |||||||||||  | || 
gtcaccctctaagttcccgtttattaaccatatatatattatttaatactgtcttgtctctatggttcttctatatatttcgtagtgtagtgattgttcggagctgtacagGTATGATATCGACATGACGAAATGCATCTATTGTGGTTTCTGCCAAGAAGCTTGCCCTGTTGATGCAATCGTGGAAGGACCAAACTTTGAGTTTGCAACC

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G79010.1 (Arabidopsis thaliana), 3'ss of exon 6
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
    ||||  | | || | | |||   ||  ||||| ||       ||||  ||||    | |        |  | | | |||    ||||||  | ||| || ||||| |||||||| |||||||||||||| || || ||||||||||||||||| || || || || || ||||| ||||||||||| ||| | || 
----gtcatca-tccctttagttc---tcatttatcaaccatc--tgctttctttattaccct--------ttcatgatgatttgagctgtatcgtacagGTACGATATCGACATGACAAAATGCATCTACTGTGGTTTCTGCCAAGAAGCTTGCCCCGTTGATGCAATCGTTGAAGGACCTAACTTTGAATTCGCAACC

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv03s0063g02550.t01 (Vitis vinifera), 3'ss of exon 6
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
                 |   |   ||| ||| ||||  | ||  | ||   |    | ||    ||   |||     ||  | |      | ||  ||| || || ||||||||||| || ||||| ||||| || || |||||||| || |||||||| || || |||||||||||||| |||||||| ||||| || 
-------------gtgatgggtcttacttggtgatctctatct--cactcactc---actcactagctcactcactagttggttta-----acttcacagGTACGACATTGACATGACCAAGTGCATTTACTGTGGATTCTGCCAAGAGGCATGCCCTGTTGATGCCATTGTGGAAGGTCCCAACTTTGAATTCACTACA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EDO96988 (Chlamydomonas reinhardtii), 3'ss of exon 5
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgta-ggcgagctctaagtttattctgcctgtatt-ttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
 ||   |  | | ||         || |||      | | | ||      |   | | |  ||  ||   |||    |  |   || | ||| |    |||| || || ||||||||||| || ||||| ||||||||||| ||||| || || ||||| |||||||| || ||||| || || ||||| |||||| | || 
gccatgcggtgacactgctgcg--cagtcgacacgattctggtgcaaaacgtcatcgtgctgtccggttggctgactgcatgcccttcatgtgtcgccgcagGTACGACATTGACATGACCAAGTGCATTTACTGCGGCTTCTGCCAGGAGGCCTGCCCCGTGGACGCGATCGTGGAGGGCCCCAACTTCGAGTTCTCTACC

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
                                |||    || |   | ||  ||| |  | ||  |  ||   ||| ||    |    |||     |||| |||||||| || ||||| || |||||||||||||| || |||||||| |||||||| || || ||||| || || || || || ||||||||  | || 
-------------------------------gtatactaagtttgtgttttcttttggttggtttgatag---taacttagcaccctttgt----cgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ15239 (Selaginella moellendorffii), 3'ss of exon 5
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgc-ctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
                              ||   |||    |||   ||  |||         |||  | |  |   | | |  || |  | | | |||| |||||||| || ||||| || |||||||||||||| || |||||||| |||||||| || || ||||| || || || || || ||||||||  | || 
------------------------------gtatactaagtttgttttttctttt---------ggctggtttgatagtaacttagcaccctttgtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC

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|162226492|gb|FC402446.1|FC402446
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|208365908|gb|DC951087.1|DC951087
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|162226685|gb|FC403770.1|FC403770
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|100407453|gb|BY991709.1|BY991709
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|208391815|gb|DC937991.1|DC937991
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|208356711|gb|DC902543.1|DC902543
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|67719791|gb|BJ970050.1|BJ970050
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|208389974|gb|DC938029.1|DC938029
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|208398252|gb|DC916419.1|DC916419
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|100407742|gb|BY955757.1|BY955757
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|208365816|gb|DC951051.1|DC951051
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|67692407|gb|BJ952640.1|BJ952640
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
EST: gi|162226684|gb|FC403769.1|FC403769
EST:     ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAG                         ATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC
genomic: ATCACTATTGAAGCAGAAGAGCGTGAAGATGGTAGTCGTCGAACCACCAGgtagtgcttg ... tattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG
 gcttgat  putative branch site (score: 5)
                            taagtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG