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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattcataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g02440.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA06G12010.1 (Glycine max), 3'ss of exon 9
--taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattc-ataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG
  ||  | ||| |||   |  |  |  ||| |     | | || ||   |||  ||   |   | |  || ||| |  |  || | |    |   |||||||| |||  |   | ||| | || ||||| |||||||| ||||||||||||||| ||||||||||||||||||||| ||| ||||| |  || | |||| |||
attatgatatctatagata--tggatataacattgttaatcaatatttcttattttttgttttgaatcaataatcatgt-gtattttcctttacctggtgcagCTTGTCGTTGATACTTTGCCATTTGGGGGAGTTGGGGAGAGTGGAATGGGTGCATACCATGGGAAGTTCTCTTTTGATGCTTTTACACACAAAAAGGCAG

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA04G42740.1 (Glycine max), 3'ss of exon 9
-taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattcataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG
 ||   | |    | |    |||||  ||     |   |     ||   | || | | ||  |    |   || |  | || | |    ||  |||||||| |||  |   | ||  | || ||||| |||||||| ||||||||||||||| ||||||||||||||||||||| ||| ||||| |  || | |||  |||
ataggcattttgcattgttatttaaa-aatccttattttctgtttcatatcaacttaaaatctgaacatttttcatgtgtattctccttttcctggtgcagCTTGTGGTTGATACCTTGCCATTTGGGGGAGTTGGGGAGAGTGGAATGGGTGCATACCATGGGAAGTTCTCTTTTGATGCTTTTACACACAAAAAAGCAG

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G26390.1 (Glycine max), 3'ss of exon 9
----taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattcataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG
    || |   |||  | |  |||| | ||    ||| || || || |   | ||    ||      ||  |  |  | ||   || |    |   |||||||| ||||||   | ||| | || ||||| |||||||| ||||||||| ||||| ||||||||||||| ||||| | ||| ||||| ||||| | |||  | |
tctatagatgctcacaattttatttaatgttttgaaataatttcaagt--gtgaacactattcacccgt--gtttctattttccatcttttttgcctggtgcagCTTGCAGTTCATACTTTACCATTTGGTGGAGTTGGTGAGAGTGGAGTGGGTGCATACCATGGGAAATTCTCATTTGAAGCTTTTAGCCACAAAAAAGCTG

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G24140.1 (Glycine max), 3'ss of exon 9
taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaa-attcataacgtagtaagaattaaattataatatgaaattgat----ggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG
  | |     | |||  || |   ||    ||| || ||  |   ||  |  |||||| ||   ||     ||   ||   || ||   ||  |    ||||||| ||||||   | ||| | || ||||| |||||||| ||||||||| ||||| ||||||||||||| ||| | | ||| ||||| ||||| | |||  |||
--agatgctcacaatttatgtattgttttgaaataatttctatctgaacactattcatcactgtgttt---tttgttttcgatttggcctttttgcctggtgcagCTTGCAGTTCATACTTTACCATTTGGGGGAGTTGGTGAGAGTGGAGTGGGTGCATACCATGGGAAATTCACATTTGAAGCTTTTAGCCACAAAAAAGCAG

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ20694 (Selaginella moellendorffii), 3'ss of exon 9
taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattcataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG
                                                ||| |    |||||  |   | |  | || | || |            ||||||||      ||||  | ||||| || || || ||  | |||||||||||  | |||||||| ||||||||||  || ||||||||||| |||||| | |
-----------------------------------------------gtaagtgtg-aacgttttgttagtggatttttgatgtttttggtccttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ32729 (Selaginella moellendorffii), 3'ss of exon 9
taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattcataacgtagtaagaat--taaattataatatgaaattgatggt--gcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG
                                                    | | |   | |||     |  |  ||| |   |||   ||| |  |  ||||||||      ||||  | ||||| || || || ||  | |||||||||||  | |||||||| ||||||||||  || ||||||||||| |||||| | |
---------------------------------------------------gtacgtgtggaagttttgttggtggattgttg-atgtttttggttcttcgcagTTTGTCACCGAGACAATGCCTTTCGGTGGCGTCGGGCACAGTGGAATGGGGGCGTACCATGGCAAGTTCTCTTTCGATGCTTTCAGCCACAGAAAGGCCG

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|34363940|gb|CF405525.1|CF405525
EST:     TGAAAACACTCTCTCCAGGGGGTTTGGTCATCAATGACACTGTTTTACAT                         TTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
genomic: TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACATgtgattaccc ... gatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
EST: gi|110361747|gb|EC925243.1|EC925243
EST:     TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACAT                         TTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
genomic: TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACATgtgattaccc ... gatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
EST: gi|110363695|gb|EC927304.1|EC927304
EST:     TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACAT                         TTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
genomic: TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACATgtgattaccc ... gatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
EST: gi|83274619|gb|DV938716.1|DV938716
EST:     TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACAT                         TTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
genomic: TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACATgtgattaccc ... gatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
EST: gi|110363431|gb|EC927016.1|EC927016
EST:     TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACAT                         TTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT
genomic: TGAAAACAGTCTCTGCAGGGGGTTTGGTCATCAATGACACTGTTTTACATgtgattaccc ... gatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaaattcataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG
          ataacgtagtaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaaaatcaataataaattttaagtaaaaaaaaaacttaaaatcgattaaattcataacgtagtaagaattaaattataatatgaaattgatggtgcagTTTGCAGAGAAGACTCTCCCTTTTGGAGGAGTTGGAGAGAGTGGAATGGGTTCATACCATGGGAAGTTCTCTTATGAGGCTTTCAGCCATAGAAAGTCAG

-aaaaaat
- - - - - - aataaat
- - - - - - - - - - - aagtaaa
- - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - cttaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatatgaa