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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgccttccaagttaagtaatttctcagtttctcacttgcagattgatctgacaataatcaattgttatcttctgtgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG

Basic information

species Physcomitrella patens
transcript PP1S180_30V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os05g05710.1 (Oryza sativa), 3'ss of exon 11
atgccttccaagttaagtaa-tttctcagtttc-tcacttgcag--attgatctgacaataatcaattgttatcttctgtgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
     ||  |  |  | ||  |||  |||||   ||||  |     |||  | | ||    ||   |  |  |  ||    || || ||   | |  | |  || ||||| |||||||||||||||||||| ||||| ||||| || ||||| ||||| ||| |||| ||||||||||| ||||| |||||  | |||||  | 
-catattaaacttctaataggtttgccagttagatcaccagtcatcattatttttacttcgattgttcatcttactcaagcaacttcgt---catcgtttccagGGATGTACACCAGAAATGGATTGAAGGCGGAAACTATGAACTTTGCATCGAAGACGTGAGGGATGAAATCTGGGACATGGTAAAGCCGGCAGATCCTCTC

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G050800_T01 (Zea mays), 3'ss of exon 4
atgccttccaagttaagtaatttctcagtttctcacttgcagattgatctgacaataat----caattgttatcttctgtgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
    |   |   ||     || |  ||  |  | |   | ||  || | |     ||||    | |||  | | |    || |     | | | ||||    |||||||| ||||||||||||||||| || || || || || || ||||| ||||||||| |||| ||||||||||| |||||||||||  | |||||  | 
--atcgaactgattgtacgatgtgccacatgat-atcagtaggctgctttctgtttaatttgaccattcatctttctcatggaaccctttttcatgtttc-cagAGATGTACACCAGAAATGGATTGAGGGCGGGAACTACGAGCTTTGCATCGAAGATGTGAGGGATGAAATCTGGGACATGGTGAAGCCCGCAGATCCTCTC

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G083459_T01 (Zea mays), 3'ss of exon 11
-atgccttccaagttaagtaatttctcagtttctcacttgcaga-ttgatctgacaataatcaat-tgttatc--ttctgtgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
 || | | | |  | | |  | |     |  ||| |  |   ||  | ||   |  ||  ||    ||  |||  |    ||  || ||| | | || | |  ||||| || ||||||||||||||||| || || || ||||| || ||||| ||||| ||| |||| ||||||||||| |||||||| ||  | |||||  | 
aattcttacaacatcatgctagt----ggaatcttatgtattgaacttattatatgatgttccccatgacatcagtatgatgctttctgttttcatgattt-cagAGACGTACACCAGAAATGGATTGAGGGAGGGAACTATGAGCTTTGCATAGAAGACGTGAGGGATGAAATCTGGGACATGGTGAAACCCGCAGATCCTCTC

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA07G38000.1 (Glycine max), 3'ss of exon 11
atgccttccaagttaagtaatttctcagtttctcacttgcagat-tgatctgacaataatcaattg-ttatcttctg--tgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
    |||  | ||    | | |   ||  |  |    |||  || | || ||||| |  |   |    | |   |||  |||   || | |           |||||||| ||||| ||||||||||| ||||| || ||||| || || || ||||||||  |||| ||||||||||||||||| |||||    |||||  | 
----ctttgacgtcccttcactggccatgtgattcgatgcgcatataatttgacattgttacttcaacttttcactgactgacccttttcttgtgaaaaaacagAGATGTACACCATAAATGGATTGAGGGTGGCAACTATGAACTTTGTATCGAAGATGTAAGGGATGAAATCTGGGATATGGTTAAGCCAGAAGATCCACTC

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA17G02700.1 (Glycine max), 3'ss of exon 10
atgccttccaagttaagtaatttctca-gtttctcacttgcagattgatctgacaataatcaattgttatcttctgtgaatt-ttgtgtacctgttctg-tagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
     ||  | ||    ||  |   || ||   ||| |       | || ||||| |  | | ||    | |||  ||| |     | | | |||      |||||||| ||||| ||||||||||| ||||| || || || || || || ||||||||  |||| ||||||||||||||||| |||||  | |||||  | 
--atttttgacgtcccttacctggccatgtgattcaatgctcatataatttgacattg-ttacttcaacttttcactgactgacccttttcttgtgaaaacagAGATGTACACCATAAATGGATTGAGGGTGGCAACTACGAACTTTGTATCGAAGATGTAAGGGATGAAATCTGGGATATGGTTAAGCCAGCAGATCCACTC

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 11
---atgccttccaagttaagtaatttctcagtttctcacttgcagattgatctgacaataat-caattgttatcttctgtgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
    |  | |    |  |||  | |  |   | ||  ||   |  |||||| ||   ||||| | |||||  |||  | ||||||   | |   |    || ||||||||||||||||||||||| |||||||| || ||||| || ||||| |||||||| || ||||| |||||||| |||||||| ||  | || || || 
cgagtctcatatctgcaaagacactagtgcatatcaaacacacc-attgatgtg-tgataatgccattgtc-tctcttctgaattc-atctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 11
--atgccttccaagttaagtaatttctcagtttctcacttgcag-attgatctgacaataatcaattgttatcttctgtgaattttgtgtacctgttctg---tagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
  || | ||   |      |   ||  ||  ||     || |||   | | ||    ||| | |||||  |    |||  |||||| |||||  | | ||    || ||||| ||||||||||||||||| || || |||||||| ||||| ||||| |||||  |||| ||||| |||||||||||||||||  | |||    | 
caatacatttggaacct--tgggttagcatgttgcagttttcagtgataacctcttcata-taaattg--actgactg-aaattttttgtactggatatgaaacagGGATGTACACCAGAAATGGATTGAGGGAGGCAATTATGAACTATGTATTGAGGATGTTAGGGATGAAATTTGGGATATGGTGAAGCCAGCTGATGAGCTA

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ29777 (Selaginella moellendorffii), 3'ss of exon 11
-----------------------------------------------------------------------------------------------atgccttccaagttaagtaattt---ctcagtttctcacttgcagattgatctgacaataatcaattgttatcttctgtgaattttgtgtacctgttct-gtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
                                                                                               |    ||||    |  | | |     | | ||    ||      || |  || |   || |     ||||     |||       || |    | | ||   || || || ||| |||||||||| ||||||||||| || ||||| ||||| || ||||||   ||||| |||||||| ||||||||||| |  |||||  | 
gttcgcctctcttactaactcaatggaagaaaagaagggtgaaagtcctagctttggcttccacttgatatgctcttccgagattcgacaggaagagtttttcctgcctgcgcactcgagacgctgtgctgcaagcctcgaatcttccgtacattactggctgttcgtcactgctctaaatgcgcctttctccttacagGGACGTGCACAAGAAATGGATCGAAGGTGGAAACTACGACCTGTGCATCGATGATGTGAAAGACGAGATCTGGGACATGGTGAAGCCGAAAGATCCTCTC

upper sequence: PP1S180_30V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ08923 (Selaginella moellendorffii), 3'ss of exon 11
-----------------------------------------------------------------------------------------------atgccttccaagttaagtaatt---tctcagtttctcacttgcagattgatctgacaataatcaattgttatcttctgtgaattttgtgtacctgttct-gtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
                                                                                               |    ||||    |  | | |     | | ||    ||      || |  || |   || |     ||||     |||       || |    | | ||   || || || |||  ||||||||| ||||||||||| || ||||| ||||| || ||||||   ||||| |||||||| ||||||||||| |  |||||  | 
gttcgtctctcttagtaactcaatggaagaaaagaagagtgaaagtcctagctttggcttccacttgatatgctcttccgagattcgacaggaagagtttttcctgcctgcgcactcgagccgctgtgctgcaagcctcgaatcttccgtatattactggctgttcgtcactgctctaaatgcgcctttctccttacagGGACGTGCACAGGAAATGGATCGAAGGTGGAAACTACGACCTGTGCATCGATGATGTGAAAGACGAGATCTGGGACATGGTGAAGCCGAAAGATCCTCTC

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|162157080|gb|FC333650.1|FC333650
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|162234572|gb|FC410838.1|FC410838
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|162234573|gb|FC410839.1|FC410839
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|162220857|gb|FC395834.1|FC395834
EST:     GACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTTTGACCTATGCATTGA
genomic: GACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|162194307|gb|FC369725.1|FC369725
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACC
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACC
EST: gi|37836901|gb|BJ594909.1|BJ594909
EST:     TTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: TTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|208349375|gb|DC918069.1|DC918069
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|37846812|gb|BJ604820.1|BJ604820
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|37841373|gb|BJ599381.1|BJ599381
EST:     TTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: TTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|162194306|gb|FC369724.1|FC369724
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
EST: gi|37853651|gb|BJ611659.1|BJ611659
EST:     CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAG                         AGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA
genomic: CTTCAGAATCGAGGCTTTTTGACGACAGTTGACGTTCACACTCTCTTCAGgtctgttctc ... tgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgacaataatcaattgttatcttctgtgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG
 atctgac  putative branch site (score: 3)
                                           cctgttct  putative PPT
        aataatcaattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgccttccaagttaagtaatttctcagtttctcacttgcagattgatctgacaataatcaattgttatcttctgtgaattttgtgtacctgttctgtagAGATGTTCACCAGAAATGGATTGAAGGTGGAAATTATGACCTATGCATTGAAGATGTGCGGGACGAAATCTGGGATATGGTGAAGCCTACCGATCCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - -cacttgc