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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgtctttattgggtctcaaatttctacattttgctccgatcataggatttacatagttaaatataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT

Basic information

species Vitis vinifera
transcript Vv07s0104g00320.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g24380.1 (Oryza sativa), 3'ss of exon 4
-atgtg-tctttattgggtctca--aatttctacattttgctccgatcataggatttacatagttaaatat-aatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
  ||   || |||    | |  |  |||| | |||| | | |    | |     ||||  | |||  |      |  | | | ||||| | |  | | | |  |||| ||||||||||| ||||||||||||||| | ||||||||  | |||||   |||   ||| ||  |||||||||| ||||| ||||| || ||||| |
cttgcaatcattacatagccataacaattacgacatgtggatttattta---actttattttgttggaagccgctagttatttttcaaattt--tgtatctgcagGTGCGTGTAAATGGTCCTGATGCTGCACCACTTTACAAATTTTTGAAAGCTAGCAAGCCTGGCTTGTTTGGATCTAGAATCAAGTGGAACTTTACCAAAT

upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G30800.1 (Glycine max), 3'ss of exon 4
atgtgtctttattgggtctcaaatttctacattttgctccg-atcataggattta-catagttaaatataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
| |||  || |||       | | |  ||||| | ||     ||   |  ||||| ||| |     | |||    | || || |||||  |||| | |  |||| ||||| ||||| |||||| | ||||| |||||||||||||| |||||| | |||   |||||||| || |||||||| || ||||||||||||||||
aagtgagtt-attcatctctatactattacatatggccgtatattccattatttagcattgggttgt-taaccgcatatattaaattcctttttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAATCAGGATTTCTGGGTTCTAGGATAAAGTGGAATTTCACCAAGT

upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G33650.3 (Glycine max), 3'ss of exon 4
atgtgtctttattgggtctcaaatttctacattttgctccgatcataggatttacatagttaaat--ataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
| |||  || ||        | |||  ||||| | ||    ||  |    | |  |   ||   |   ||||  || || || |||||  |||| | || |||| ||||| ||||| |||||| | ||||| |||||||||||||| |||||| | ||||  |||||||| ||   |||||| || ||||||||||| ||||
aagtgagtt-atgcatctctatattattacatat-gcctgtattgtccattatttagcattgggttgttaattgtatatattaaattcctttttatttacagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAAACAGGATTTCTGGGTAGTAGGATAAAGTGGAATTTCACTAAGT

upper sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G63080.1 (Arabidopsis thaliana), 3'ss of exon 4
------------atgtgtctttattgggtctcaaatttctacattttgct-ccgatcataggatttacatagttaaatataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
            |   | |  | ||     ||| ||  ||  | |  |   | |||  |   | ||  |||  |||  || |      ||| |||  | | | | |||| ||||| ||||||||||| |   | ||||||||||||||||||||||||||| |  | |||      |||||||||  | | ||||||||||| ||||||||||
gtacctcaacaaacaagacacttttcttcttcatatgcctttaataggtagctgattttgtaagtt-tataactaagcatgaatgatcatgatcatctatgtgt-gtgtgtagGTGCGTGTAAATGGACAAAACGCTGCACCAGTCTACAAATTCCTCAAATCTAAGAAACCCTCTTTTCTTGGAAGTCGTATCAAATGGAACTTCACCAAGT

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|32270831|gb|CD719990.1|CD719990
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|18458555|gb|BM436833.1|BM436833
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|71871438|gb|DT020493.1|DT020493
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|33406214|gb|CF211841.1|CF211841
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|110715122|gb|EE092811.1|EE092811
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAACA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|32248717|gb|CD714536.1|CD714536
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|32247920|gb|CD713739.1|CD713739
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|32270478|gb|CD719637.1|CD719637
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|30320455|gb|CD003717.1|CD003717
EST:     AAGAATTTGCATGTACAAGATTCAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|30321053|gb|CD004315.1|CD004315
EST:     GAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTGTACAAATTCCTCAAAGCA
genomic: GAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|110385668|gb|EC950213.1|EC950213
EST:     CAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: CAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|30327074|gb|CD010336.1|CD010336
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|30326869|gb|CD010131.1|CD010131
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|30325093|gb|CD008355.1|CD008355
EST:     GAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: GAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|110730026|gb|EE106638.1|EE106638
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|110360010|gb|EC922487.1|EC922487
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|22010087|gb|BQ795121.1|BQ795121
EST:     AATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|32268850|gb|CD718009.1|CD718009
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|32268634|gb|CD717793.1|CD717793
EST:     GAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: GAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|33406296|gb|CF211923.1|CF211923
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|110374752|gb|EC939679.1|EC939679
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|30325164|gb|CD008426.1|CD008426
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
EST: gi|110360267|gb|EC923156.1|EC923156
EST:     AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAG                         GTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA
genomic: AAGAATTTGCATGTACAAGATACAAGGCTGAATATCCAATTTTTCATAAGgtaaaagaaa ... ttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggatttacatagttaaatataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
                                 ttcaattctctttt  CT-rich tract
     tttacatagttaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgtctttattgggtctcaaatttctacattttgctccgatcataggatttacatagttaaatataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - -ttgctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatata