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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactctctgtcaataatctccaaatacttcaaaaattgttcacagaatttcctaaatttatcagaaatctttgtcacctaaaagttatcagacgcaagggtcagttttacttacgcatcgatctacttgtctgcagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCTTTTCACCTCTGCCCGCTTGAAGAAAGGGGAAGTTTTGTACTTAGAAACT

Basic information

species Arabidopsis thaliana
transcript AT5G08450.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 8
gtaactctctgtcaataatctccaaatacttcaaaaattgttcacagaatttcctaaatttatcagaaatctttgtcacctaaaagttatcag---acgcaagggtcagttttacttacg--catcgatctacttgtctg-cagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCTTTTCACCTCTGCCCGCTTGAAGAAAGGGGAAGTTTTGTACTTAGAAACT
                                           |    ||  |    ||  | || | || |||  || || |  || || ||   |   |    |||  | |||| | |   ||    ||  || | || |||||| || ||||| ||||||| ||||||||| || ||| | || ||||| |||| ||| ||||| || |||||||| |||||||||||||| || || || 
------------------------------------------aattagatacctggcatgcaacacatattttt--cagcttactgtgattagtttataaacctatcatctatactcatgattataatactttttatttgtcagGATAAAGTATAGTATAAGCACTGTTGCTGACAAGGGTTTAAAAAAGCCACTTTACACATCTGCACGTTTGAAGAAGGGGGAAGTTTTGTATTTGGAGACA

upper sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 8
gtaactctctgtcaataatctccaaatacttcaaaaattgttcacagaatttcctaaatttatcagaaatctttgtcacctaaaagttatcagacgcaagggtcagttttacttacgcatcgatctacttgtctgcagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCTTTTCACCTCTGCCCGCTTGAAGAAAGGGGAAGTTTTGTACTTAGAAACT
                             |       ||  |||   |  |   | |||  | |||   | |||||  | ||    || |     | |    | |  |  ||| |   ||     ||||| ||   ||||| |||||||| ||||||||||||||||| || ||||| || ||||| || |  || ||||| || || ||||| || |||||| | ||  | || || 
-----------------------------tcttgttcttcctcatttagata--tgaatgcaacagttctatttgtagcttatc--ttgtttttagtatttattaact--actaattaattataatacttatc---agGATCAAATATAGTATAAGCATTGTTGCTGACAAGGGTCTAAAAAAGCCACTCTATACATCTGCTCGTTTAAAGAAGGGAGAAGTTCTTTATCTGGAGACA

upper sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 7
gtaactctctgtcaataatctccaaatacttcaaaaattgttcacagaatttcctaaatttatcagaaatctttgtcacctaaaagttatcagacgcaagggtcagttttacttacgcatcgatctacttgtctg-cagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCTTTTCACCTCTGCCCGCTTGAAGAAAGGGGAAGTTTTGTACTTAGAAACT
                                     ||||||      |    || || |    | ||   || |    |  |  || ||         | |   | ||| |||   ||  ||    |||  |  |||||| |||||||| ||||||||||||||||| || ||||| || ||||| || |  || ||||| || || ||||| || |||||| | ||  | || || 
------------------------------------cttgttcttcc--tcatttagatatgaatgcaacagttctattttgtagcttgtcttgtttttag-tatttattaattaataattaattatattgcttatcagGATCAAATATAGTATAAGCATTGTTGCTGACAAGGGTCTAAAAAAGCCACTCTATACATCTGCTCGTTTAAAGAAGGGAGAAGTTCTTTATCTGGAGACA

upper sequence: AT5G08450.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 8
gtaactctctgtcaataatctccaaatacttcaaaaattgttcacaga-atttcctaaatttatcagaaatctttgtcacctaaaagttatcagacgcaagggtcagttttacttacgcatcgatctacttgtctgcagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCTTTTCACCTCTGCCCGCTTGAAGAAAGGGGAAGTTTTGTACTTAGAAACT
                           |   |||  | |       ||  |||  |   ||  |  ||    | | ||   ||||   |    |  |     |||| ||||       |||   |  |    | | |||||||||||| |||||||||||||||||||| ||||| || |||||||| ||||  || ||||| ||||||||||| || ||||||||||| |||||||| 
--------------------------gatagcaaggactaacatttgatgttttatgggttcctttga---ttctatcttttaaa---tgaatggtgttctcgtcaatttt-------catgcttgcaaaaatgtacagGATTAAATACAGCATAAGCATTGTTGCTGACAAAGGCCTAAAGAAGCCCCTTTATACATCTGCACGCTTGAAGAAGGGAGAAGTTTTGTATTTAGAAACA

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|164068506|gb|ES199837.1|ES199837
EST:     AGG-TTGTACGAGAAGTCACAATACAATACAATCTCTGCAATGAACCTTG                         GATTAAATATAGCATAAGCATTGTTG
genomic: AGGTTTGTACGAGAAGTCACAATACAATACAATCTCTGCAATGAACCTTGgtaactctct ... ttgtctgcagGATTAAATATAGCATAAGCATTGTTG
EST: gi|116448742|gb|EG491334.1|EG491334
EST:     CTGCAATGAACCTTG                         GATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCT
genomic: CTGCAATGAACCTTGgtaactctct ... ttgtctgcagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttatcagacgcaagggtcagttttacttacgcatcgatctacttgtctgcagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCTTTTCACCTCTGCCCGCTTGAAGAAAGGGGAAGTTTTGTACTTAGAAACT
                          tacttac  putative branch site (score: 1)
                                        tctactt  putative PPT
                       ttttactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactctctgtcaataatctccaaatacttcaaaaattgttcacagaatttcctaaatttatcagaaatctttgtcacctaaaagttatcagacgcaagggtcagttttacttacgcatcgatctacttgtctgcagGATTAAATATAGCATAAGCATTGTTGCTGATAAAGGTCTCAAGAAGCCTCTTTTCACCTCTGCCCGCTTGAAGAAAGGGGAAGTTTTGTACTTAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA