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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtccatgatggtctcttggacatttcttctcttcgggcctagatccactcatcacccatcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG

Basic information

species Arabidopsis thaliana
transcript AT5G66120.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 5
-------------gtaagtagtccatgatgg-tctcttggacatttcttctcttcggg----cctagat-ccactcatcacccatcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG
              |  ||     |   |   | || |  ||| ||  | |  |   |    |||| ||   | | || | |  |   || | ||  ||||| |||||||| ||   |||||||||||  ||||||||||| || |||||||||||||| || 
ttaattcaaatatatgggtgccagaaactaaatatcctcaacagtttgtttaatgatgtactcctacatattatttatgatcactttattcaattgccagGCTATAGAAACAGGAACTGGTTATGGAGCATGGCTCCATGGGGAGGCTGTTGCAGCTGGAACA

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G36890.1 (Glycine max), 3'ss of exon 5
-----------------------gtaagtagt--ccatgatggtctcttggacatttcttctcttcgggcctagatccactcatcacccatcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG
                         || | ||  |     |   || ||    |  | |||   || |   |  |  |  ||    |    |||||| |||   |||| |||||||||||  |||| |||||  ||||||| |||||||| ||||||||||||||||||
ctgtgacatcaaactattcccaaaaaaattgtttctgcattctccttttcagtaaattttcctctctgattttaactctttcc---cgtggcacttatttt---agGCAATAGAAACTGGGGTTGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 5
-----------------------gtaagtagtccatgatggtctcttggacatttcttctcttcgggcctagatccactcatcacc-catcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG
                        ||| | ||   ||       |||   | |   || || ||   | ||     |||| |  ||    |||||| |||   |||| |||||||||||  | || |||||  ||||||| |||||||| ||||||||||||||||||
tgtgacatcaaactattcccaaaataaattgtttctggattctccttttccgtaaattttcctct--cttattattactctttcccgtggcacttatttt---agGCAATAGAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G08350.2 (Glycine max), 3'ss of exon 5
----------------gtaagtagtccatgatggtctcttggacatttcttctcttcgggcctagatccactcatcacc-catcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG
                 ||| | ||   ||       |||   | |   || || ||   | ||     |||| |  ||    |||||| |||   |||| |||||||||||  | || |||||  ||||||| |||||||| ||||||||||||||||||
tcaaactattcccaaaataaattgtttctggattctccttttccgtaaattttcctct--cttattattactctttcccgtggcacttatttt---aggcaatagAAACTGGGGTAGGCTATGGGCAGTGGCTTCATGGAGAGGCTGTTGCAGCTGGCACG

upper sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 5
-----gtaagtagtccatgatggtctcttggacatttcttctcttcgggcctagatccactc------atcac-------ccatcacttaattt-tgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG
      | || ||    |  | ||      | |   | || | ||         | || ||       ||| |         ||||| |  ||| | ||||| |||||||||||  ||||||||||  ||||||||||||||||||||||||||||||||| |
ttggtttgaggagcttttagttgttatccagtcccatgttatatttaccaaagaaacccctttaagcaatcccattctgattatcacatcttttcttcagGCAATAGAAACTGGGGTTGGTTATGGGCAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCATG

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|116478278|gb|EG520870.1|EG520870
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGA
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGA
EST: gi|116450338|gb|EG492930.1|EG492930
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
EST: gi|116421960|gb|EG464552.1|EG464552
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
EST: gi|124801153|gb|EH890628.1|EH890628
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGA
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGA
EST: gi|125267934|gb|EL282019.1|EL282019
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTTGGTT
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTT-GGTT
EST: gi|116421951|gb|EG464543.1|EG464543
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
EST: gi|125323959|gb|EL338039.1|EL338039
EST:     AAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
genomic: AAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
EST: gi|116421921|gb|EG464513.1|EG464513
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
EST: gi|116472854|gb|EG515446.1|EG515446
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
EST: gi|125013457|gb|EL085726.1|EL085726
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAAC
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAAC
EST: gi|124735304|gb|EH826706.1|EH826706
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAAC
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAAC
EST: gi|116421964|gb|EG464556.1|EG464556
EST:     AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCAT                         GCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT
genomic: AAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagtc ... aattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatttcttctcttcgggcctagatccactcatcacccatcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG
                                         acttaat  putative branch site (score: 4)
                                         acttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagtccatgatggtctcttggacatttcttctcttcgggcctagatccactcatcacccatcacttaattttgcagGCCATAGAAACTGGCTTTGGTTATGGAGAGTGGCTCCATGGAGAAGCTGTTGCAGCTGGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG