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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctaattctatattcttttctatgctatttcagtcagtgtatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT

Basic information

species Vitis vinifera
transcript Vv17s0000g06640.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 16
-------------gttctaattctatattcttttctatg-----ctatttcagtcagtgtatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT
              |   ||    ||  | |||| | ||     |  |   ||| | |||| ||  ||      | ||||  || | |     ||||||||||||||||||||| |||||||||||||||||||| || || | ||| || |||||||| || ||||||||   ||||||| |||||||||| ||||| |
atctgcacttttaatgaaaagaaaatgcttttttttctggctgtcagtaatagttaatgtaattgcaatgaatagtgatcataaattcctgatcttgcagATACAATTGAAATCATTAGCAGAAGAAATGCAGGCAATCATCAGGGGATTAGAAAAGGTTAAACAGGAGCTTGCTGCATCTAAAAATGATGGCCCTGTGT

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA04G32990.1 (Glycine max), 3'ss of exon 17
--------------------gttctaattctatattcttttctatgctatttcagtcagtgtatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT
                     |  |  || ||  |   |  || | |  | | ||| | | |  ||  ||      | ||||  || | |     ||||||||||||||||||||| |||||||||||||||||||| || || | ||| || |||||||| || ||||||||   ||||||| |||||||||| || || |
tcacttttaacgaaaagaaaatgttgtttgtac-tagctaactgt-cagtattagttaatctgattgcaatgaatagtgatcgtaaattcctgatcttgcagATACAATTGAAATCATTAGCAGAAGAAATGCAGGCAATCATCAGGGGATTAGAAAAGGTTAAACAGGAGCTTGTTGCATCTAAAAATGATGGCCCCGTGT

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 14
------------------gttctaattctatattcttttctatgctatttcagtcagtg-tatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT
                   |  | |      | | |||    | |    ||||  | |  ||||   | |  ||| | |   ||    |  || ||| |||||||||||||| || ||||||||||| |||||||| || || ||||| || |||||||| || || ||  |   |||||||| ||||||||| ||||| |
tttagctgaaagaaacagctgttgagatgggactgtttaaattccagcatcaggtaataatattacaatggttattg-actggacacaccatttctttcagATACAATTGAAGTCATTAGCAGAAGAGATGCAGGCAATCATCAAGGGATTAGAAAAGGTTAAACAAGAATTTGCTGCATCTGCAAATGATGGACCTGTCT

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 16
-----------------gttc-taattctatattcttttctatgctatttcagtcagtg-tatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT
                  | | |       |   |  || ||  | |||| ||  | |  ||||     |  ||| | |   ||  |||  || ||| |||||||||||||| || ||||||||||| |||||||| || || ||||| || |||||||| || || ||  |   |||||||| ||||||||| ||||| |
attatgattatgtttggatgcatggacgggtcacccattataacccattttaggtaataatattacactggttattg-actggacatgccatttctttcagATACAATTGAAGTCATTAGCAGAAGAGATGCAGGCAATCATCAAGGGATTAGAAAAGGTTAAACAAGAATTTGCTGCATCTGCAAATGATGGACCTGTCT

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 13
-gttctaattctatattcttttctatgctatttcagtcagtgtat-ttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT
  ||  | || |  |||  |     | ||| | |  | ||| | | || |   |  ||  ||||     | |  |   ||||||||||||||||| ||| | || || |||||||| |||||||| || || ||||||||  | || |||||||| | |||||| |||| |||||||||||| |
gtttgcagttgttcatttctcgtcct-ctactcc--ttagtttctattggctcatcatttgatcg----tcctgtctattgcagATACAATTGAAGTCTCTGGCTGAGGAAATGCAAGCTATAATCAAAGGATTGGAAAAACTGAACCAGGAGCTCACTGCATCCGAAAGTGATGGTCCTGTTT

upper sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT5G07780.1 (Arabidopsis thaliana), 3'ss of exon 10
gttctaattctatattcttttcta--tgctatttcagtc--agtgtatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT
            | ||| ||||||  | || |||| |||    |||| || |   |  ||  ||| ||   ||   |   ||||||||||| ||||| ||||| || || ||||| || |||||||  || || ||||||||  | ||||||||||| |  ||||| |||| |||||||||||| |
-----------gttttcctttctacttactttttccgtcctgctgtaattggctcatcatttgat-tgtcctg---tctattgcagATACAGTTGAAGTCTTTGGCTGAGGAAATACAAGCTATAACCAAAGGATTGGAAAAACTGAAGCAGGAGCTTACCGCATCCGAAACTGATGGTCCTGTTT

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|110700830|gb|EE077830.1|EE077830
EST:     GACTTCTAGATTTCCATGAGGATCTTGTTAGCCTGGAGGCTGCATCAAAG                         ATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG
genomic: GACTTCTAGATTTCCATGAGGATCTTGTTAGCCTGGAGGCTGCATCAAAGgttctaattc ... ttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG
EST: gi|110700821|gb|EE077821.1|EE077821
EST:     GACTTCTAGATTTCCATGAGGATCTTGTTAGCCTGGAGGCTGCATCAAAG                         ATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG
genomic: GACTTCTAGATTTCCATGAGGATCTTGTTAGCCTGGAGGCTGCATCAAAGgttctaattc ... ttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG
EST: gi|110700879|gb|EE077921.1|EE077921
EST:     GACTTCTAGATTTCCATGAAGATCTTGTTAGCCTGGAGGCTGCATCAAAG                         ATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG
genomic: GACTTCTAGATTTCCATGAGGATCTTGTTAGCCTGGAGGCTGCATCAAAGgttctaattc ... ttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG
EST: gi|110700824|gb|EE077817.1|EE077817
EST:     GACTTCTAGATTTCCATGAGGATCTTGTTAGCCTGGAGGCTGCATCAAAG                         ATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG
genomic: GACTTCTAGATTTCCATGAGGATCTTGTTAGCCTGGAGGCTGCATCAAAGgttctaattc ... ttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcagtcagtgtatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT
                                          cgcttcctt  CT-rich tract
              tatttagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctaattctatattcttttctatgctatttcagtcagtgtatttagaagactatgggatctgaattgcgcttccttgcagATACAATTGAAATCTTTAGCAGAAGAAATGCAGGCTATAATGAAGGGGTTGGAAAAGGTCAAGCAGGAGCTGAATGCATCTGAAAATGATGGTCCTGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA