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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacttagttatctgattttaggattatagaatttctgttgtccatgtttcttttgccttatgttgaaagttttcttttttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG

Basic information

species Vitis vinifera
transcript Vv08s0007g00530.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G15960.1 (Glycine max), 3'ss of exon 2
----------------------------------------------gtaactacttagttatc-tgattttaggattatagaatttctgttg-tccatgtttcttttgccttatgttgaaagttt----tcttttttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
                                               | ||   ||    ||  ||  |||| | |||   ||||  | |   |  ||    ||||||  | || ||  || |||      ||||| || ||||||||||||||||||||| || |||||||||||||| |
gtactattatagtttctgcattatgcatttatgcttaagttaacctattacagtttctgcattatgcatttatgcttaagtaattcttttaaatttatcccccttttgattcatattttaattttaatgattttttcatattagGTTGACTGGATTGGGCAGAAAAATCAAATAGATGTCG

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G39930.1 (Glycine max), 3'ss of exon 2
gtaactacttagttatctgattttaggattatagaatttctgttgtccatgtttcttttgccttatgttgaaagttttcttttttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
   |||| |    | ||||   |||   |||   | ||| |    |  ||    |||||   | || ||  ||  |   ||||  || ||||||||||||||||||||| || |||||||||||||  |
--tactattacagtttctg-cattattcttaagtatttttttaaatttatccccctttttattcatattttaa--tgatttttacatattaggTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G39930.2 (Glycine max), 3'ss of exon 2
gtaactacttagttatctgattttaggattatagaatttctgttgtccatgtttcttttgccttatgttgaaagttttcttttttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
||| ||| |    | ||||   |||   |||   | ||| |    |  ||    |||||   | || ||  ||  |   ||||  || ||||||||||||||||||||| || |||||||||||||  |
gta-ctattacagtttctg-cattattcttaagtatttttttaaatttatccccctttttattcatattttaa--tgatttttacatattagGTTGACTGGATTGGGCAGAAAAATCAAATAGATGCCG

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|349811666|gb|FQ409663.1|FQ409663
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|349810529|gb|FQ402772.1|FQ402772
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|351016336|gb|FQ446196.1|FQ446196
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|349821239|gb|FQ404371.1|FQ404371
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|110700744|gb|EE077667.1|EE077667
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|110385557|gb|EC950093.1|EC950093
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|352786365|gb|FQ478974.1|FQ478974
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|45771772|gb|CN007624.1|CN007624
EST:     TTCCTGAGCA-                         GTTGACTGGA-T-GGCAAAA-AATTAAATAGATG-TG
genomic: TTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|351023663|gb|FQ448214.1|FQ448214
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|352790186|gb|FQ481385.1|FQ481385
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|351051751|gb|FQ449565.1|FQ449565
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|351054211|gb|FQ450293.1|FQ450293
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|351028714|gb|FQ433144.1|FQ433144
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|110692043|gb|EE070833.1|EE070833
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
EST: gi|351055225|gb|FQ440564.1|FQ440564
EST:     AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAG                         GTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
genomic: AAGGTCAAAGGCCAGAGTTTTATTTTGAAGAAGGAGCCTTTCCTGAGCAGgtaactactt ... tttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttgtccatgtttcttttgccttatgttgaaagttttcttttttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG
                                     ttttcttttttatgtt  CT-rich tract
                                 aaagttttctttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactacttagttatctgattttaggattatagaatttctgttgtccatgtttcttttgccttatgttgaaagttttcttttttatgttagGTTGACTGGATTGGGCAAAAGAATCAAATAGATGTTG

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