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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgagtctcatatctgcaaagacactagtgcatatcaaacacaccattgatgtgtgataatgccattgtctctcttctgaattcatctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA

Basic information

species Arabidopsis thaliana
transcript AT5G18580.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os05g05710.1 (Oryza sativa), 3'ss of exon 11
cgagtctcatatctgcaaagacactagtgcatatcaaacacaccattgatgtgtgataatgccattgtctctctt-ctgaattcatctgttta--acttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA
    | | | |  |  ||      |      ||    ||    |||   | | |  || | | |||||   |||| || ||   |  |  | |    || ||| ||||| |||||||||||||| ||||| || ||||||||||| ||||| ||||| ||  | || || |||||||||||||| || ||| | || ||  | 
--catattaaacttctaataggtttgccagttagatcaccagtcatcattatttt-tacttcgattgttcatcttactcaagcaacttcgtcatcgtttccagGGATGTACACCAGAAATGGATTGAAGGCGGAAACTATGAACTTTGCATCGAAGACGTGAGGGATGAAATCTGGGACATGGTAAAGCCGGCAGATCCTCTC

upper sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G083459_T01 (Zea mays), 3'ss of exon 11
cgagtctcatatctgcaaagacactagtgcatatcaaacacacca---ttgatgtgtgataatgccattgtctctcttctgaattcatctgttta---acttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA
  | ||| | | |  ||      |||||| | |||  |   |      ||  | | ||||  | ||  || |     | |||     |||||||      || |||||| || |||||||||||||| || || ||||||||||| || ||||||||||| ||  | || || ||||||||||||||||||||  | || ||  | 
-aattcttacaacatca----tgctagtgga-atcttatgtattgaacttattatatgatgttccccatgacatcagtatgatgctttctgttttcatgatttcagAGACGTACACCAGAAATGGATTGAGGGAGGGAACTATGAGCTTTGCATAGAAGACGTGAGGGATGAAATCTGGGACATGGTGAAACCCGCAGATCCTCTC

upper sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G050800_T01 (Zea mays), 3'ss of exon 4
--cgagtctcatatctgcaaagacactagtgcatatcaaacacaccattgatgtgtgataatgccatt-gtctctcttctgaattcatctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA
  |||      | |  |    | |||  |   ||||||         ||  ||| | ||    |||||  ||| |||  || |  | | | |     || ||||||||| |||||||||||||| || || |||||||| || || ||||| ||||||||  | || || ||||||||||||||||| ||  | || ||  | 
atcgaactgattgtacgatgtgccacatg---atatcagtaggctgctttctgtttaatttgaccattcatctttctcatggaaccctttttcatgtttccagAGATGTACACCAGAAATGGATTGAGGGCGGGAACTACGAGCTTTGCATCGAAGATGTGAGGGATGAAATCTGGGACATGGTGAAGCCCGCAGATCCTCTC

upper sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G38000.1 (Glycine max), 3'ss of exon 11
cgagtctcatatctgcaaagacactagtgcatatcaaacacaccattgatgtgtgataatgccattgtctctcttctgaat-tcatctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA
    |  | |  || ||  | |  |             || |  |||      || || | | | | |       ||||   |  |||  | ||    ||||||||| ||||| |||||||| || ||||| ||||||||||| || || ||||||||  | || || |||||||| ||||| || ||    || ||| | 
-ctttgacgtcccttcactggccatgtgattcgatgcgcatataatttgacattgttacttcaacttttcactgactgacccttttcttgtgaaaaaacagAGATGTACACCATAAATGGATTGAGGGTGGCAACTATGAACTTTGTATCGAAGATGTAAGGGATGAAATCTGGGATATGGTTAAGCCAGAAGATCCACTC

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

upper sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ29777 (Selaginella moellendorffii), 3'ss of exon 11
-----------------------------------------------------------------------------------------------cgagtctcatatctgca-----aagacactagtgcatatcaaacacaccattgatgtgtgataatgccattgtctctcttctgaattcatctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA
                                                                                                |  | || |  ||||       |||| ||       |     |  | | |   |   | |        | ||| ||  ||| ||| |  || ||   ||| ||| || || ||| |||||||||| |||||||| ||||| || |||||||| || |||||   |||||||||||||||||||||||| |||   || ||  | 
gttcgcctctcttactaactcaatggaagaaaagaagggtgaaagtcctagctttggcttccacttgatatgctcttccgagattcgacaggaagagtttttcctgcctgcgcactcgagacgctgtgctgcaagcctcgaatcttccgtacattactggctgttcgtcactgctctaaatgcgcct-ttctccttacagGGACGTGCACAAGAAATGGATCGAAGGTGGAAACTACGACCTGTGCATCGATGATGTGAAAGACGAGATCTGGGACATGGTGAAGCCGAAAGATCCTCTC

upper sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ08923 (Selaginella moellendorffii), 3'ss of exon 11
-----------------------------------------------------------------------------------------------cgagtctcatatctgcaaagaca--ctagtgcatatcaaacac---accattgatgtgtgataatgccattgtctctcttctgaattcatctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA
                                                                                                |  | || |  ||||  |  |   |   ||     ||| |     | | |   | | | |        | ||| ||  ||| ||| |  || ||   ||| ||| || || |||  ||||||||| |||||||| ||||| || |||||||| || |||||   |||||||||||||||||||||||| |||   || ||  | 
gttcgtctctcttagtaactcaatggaagaaaagaagagtgaaagtcctagctttggcttccacttgatatgctcttccgagattcgacaggaagagtttttcctgcctgcgcactcgagccgctgtgctgcaagcctcgaatcttccgtatattactggctgttcgtcactgctctaaatgcgcct-ttctccttacagGGACGTGCACAGGAAATGGATCGAAGGTGGAAACTACGACCTGTGCATCGATGATGTGAAAGACGAGATCTGGGACATGGTGAAGCCGAAAGATCCTCTC

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|116425494|gb|EG468086.1|EG468086
EST:     CTCCAAGGGAGAGGCTTTCTCACTACTGCTGATATTCACTCTCTTTTCAG                         AGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGA
genomic: CTCCAAGGGAGAGGCTTTCTCACTACTGCTGATATTCACTCTCTTTTCAGgtaatgaatc ... taacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGA
EST: gi|116425496|gb|EG468088.1|EG468088
EST:     CTCCAAGGGAGAGGCTTTCTCACTACTGCTGATATTCACTCTCTTTTCAG                         AGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGA
genomic: CTCCAAGGGAGAGGCTTTCTCACTACTGCTGATATTCACTCTCTTTTCAGgtaatgaatc ... taacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGA
EST: gi|124860338|gb|EH944775.1|EH944775
EST:     CTCCAAGGGAGAGGCTTTCTCACTACTGCTGATATTCACTCTCTTTTCAG                         AGATGTTCACCAGAAATG
genomic: CTCCAAGGGAGAGGCTTTCTCACTACTGCTGATATTCACTCTCTTTTCAGgtaatgaatc ... taacttgcagAGATGTTCACCAGAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgtgtgataatgccattgtctctcttctgaattcatctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA
                                          gtttaac  putative branch site (score: 3)
                                       tctgttt  CT-rich tract
                                           tttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgagtctcatatctgcaaagacactagtgcatatcaaacacaccattgatgtgtgataatgccattgtctctcttctgaattcatctgtttaacttgcagAGATGTTCACCAGAAATGGATAGAAGGTGGGAACTATGAACTGTGCATAGAAGATGTTCGAGACGAGATCTGGGACATGGTGAAACCGTCTGACCCATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - -caaagac
- - - - - - - - - - - - - - - - - caaacac