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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacttattgctataatgttttttatttatttggtttcttgacattgaacatctcttatctcttggtgtcatcaagATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG

Basic information

species Arabidopsis thaliana
transcript AT5G18590.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18590.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G38020.1 (Glycine max), 3'ss of exon 9
-------------------------------gtaatacttattgctata--atgttttttatttatttggtttcttgacattgaacat---ctctt-----atctcttggtgtcatcaa----------------gATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG
                                |  |   || ||| |||  |||   | ||  |  ||| |||||  ||| || | ||    | ||     | |  ||  | |  | ||                ||||| ||||||| || |||||||| |||| ||||| |||||||| ||||| ||| ||||||  || ||||| ||||||||||||||||| || || || |
gtgagggagctctgtaggtccaaatgtgtcaatggtctatactgcaataacatgcagtataactgcttgatttctctacagtgcaaatgaatttttcgtagaccatttaatttgctaaaaatttatatttcttcagATGGCATGGTCACGAGTAAAGATACGAGGTTTTCATCCATCACCTAGAGCTGGTTGTTGTGACGTCCTTTGTGGTACTAAATGGTATATCACTGGGGGTG

upper sequence: AT5G18590.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G28760.1 (Glycine max), 3'ss of exon 8
----gtaatacttattgctataatgttttttatttatttggtttcttgac--attgaacatctcttatct--cttggtg-----------tcatcaagATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG
    |   |   |||   |  ||  |||||||||| |      |   ||   | ||  |||   || | |   ||  ||           || |  |||||| ||||||||||||||| ||| | || || || |||||||||||||| ||| | ||||| ||| | || || |||||||||||||| || ||||| |
gtgagctctctatatcagtgaaac-ttttttatttctccaaaatgaagattaaatgctcattcattgtgtaatttaatgaaagtatattttctttcagATGGCATGGTCAAGAATAAAAATACGTGGTTTCCATCCATCACCAAGAGCTGGTTGCTGTGGTGTTTTATGTGGCACTAAATGGTATATTACAGGAGGTG

upper sequence: AT5G18590.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G02680.1 (Glycine max), 3'ss of exon 8
-------------------------------gtaatacttattgctata--atgttttttatttatttggtttcttgacattgaacat---ctctt-----atctcttggtgtcatcaa--------------------gATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG
                                |  |   ||  |  |||  |||   | ||  |  ||| |||||  ||| || | ||    ||||     | |  ||  | | || ||                    ||||| ||||||| || | |||||  |||| ||||| || ||||| ||||| ||| ||||||| || ||||| ||||||||||||||||| || || || |
gtgagtgagctctgtaggtccaaatgtgtcaatggtctatacagaaataacatgcagtataactgcttgatttctccacagtgcaaatgaattcttcataaaccatttaatttgataaaaatatatatatatttcttcagATGGCATGGTCACGAGTGAAGATGCGAGGTTTTCATCCGTCACCTAGAGCTGGTTGTTGTGGTGTCCTTTGTGGTACTAAATGGTATATCACAGGTGGTG

upper sequence: AT5G18590.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G10310.1 (Glycine max), 3'ss of exon 10
gt-aatacttattgctat-aatgttttttatttatttggtttcttgac--attgaacatctcttatct--cttggtg-----------tcatcaagATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG
|| |   || ||  |  | ||  |||||||||| |      |   ||   | ||  |||   || | |   ||  ||           || |  |||||| ||||||||||||||| |||   || || || |||||||||||||| ||| | ||||| ||| | || || |||||||||||||| || || || |
gtgagctctcatatcagtgaaacttttttatttctccaagatgaagattaaatgctcattcattgtgtaatttaatgaaagtatatgttctttcagATGGCATGGTCAAGAATAAAAATACATGGTTTCCATCCATCACCAAGAGCTGGTTGCTGTGGTGTTTTATGTGGCACTAAATGGTATATTACAGGGGGTG

upper sequence: AT5G18590.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0020g01740.t01 (Vitis vinifera), 3'ss of exon 10
---------------------gtaatacttattgctataatgttttttatttatt----tggtttcttga-----cattgaacatctcttatctcttggtgtca--tcaagATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG
                      |     ||||||  | |    ||| | | |||     ||    |||       ||||       | | || | | | | |       ||||| ||||||||||||| ||||  | | ||      |||||||| ||||| ||| ||||||||||| | || || ||||||||||||||| | || || |
gtttgtagagcaaccattcttctggagtttattgtcaaacaactttatttctataatgatgaaaacttacatcttcattagttgattttgatatgtggatttttgtctcagATGATATGGTCAAGAATTAAGAAGAAACGAGGATTTCCATCACCTAGAGCTGGTTGTTGTGGAGTTTTATGTGGAACTAAATGGTATATAGCAGGGGGTG

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|125191602|gb|EL206556.1|EL206556
EST:     GGGCAAGAACAAAACACTAAATGTACTTATACTCACTCGACTTTGAAACG                         ATGGTATGGTCAAGAAATAAAGATAAGAGGATTTCACCCATCACCAAGAGC
genomic: GGGCAAGAACAAAACACTAAATG-ACTTATACTCACTCGACTTTGAAACGgtaatactta ... tgtcatcaagATGGTATGGTCAAGAA-TAAAGATAAGAGGATTTCACCCATCACCAAGAGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttatttggtttcttgacattgaacatctcttatctcttggtgtcatcaagATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG
               tcttgac  putative branch site (score: 3)
     ttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacttattgctataatgttttttatttatttggtttcttgacattgaacatctcttatctcttggtgtcatcaagATGGTATGGTCAAGAATAAAGATAAGAGGATTTCACCCATCACCAAGAGCGGGTAGTTGTGGAGTTCTTTGCGGTACTAAATGGTATATAACCGGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG