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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT

Basic information

species Vitis vinifera
transcript Vv12s0035g01130.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G00470.4 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------gcctagttgataa--gttgcta---tggttgctctgttttctacttctcattcttcaagg---tttaaaactttga----agttcacaatgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
                                                                   |||   ||||   |||| |   | |||    ||  |  |   ||  | | || ||     | | | ||   ||    || ||    |||||    |  | ||  ||||||||| ||||||||||| |||||||||||||||||||| ||||| ||||||||||||||||| ||||||||||| || || || || ||  ||||||||||
gtattgtttttgtgtcccccctgtgggttcattgttttaaatgtttcctaaattaggattgtgattatagcctataatcattgcaaaattagttatgatgaatcttctctcagaattttaaaaaaattatgacacccagagttgagatctttttgaatccactttttatcttgcagGATTTTGGGACATGTATGATCCCGAGGGATACTCTCTCTGGTTTTGTGATTACAAATACAACGACGAGAATACTGTTTCTTTTGTGACATTGAACAAGGT

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G00360.1 (Glycine max), 3'ss of exon 6
gcctagttgataagttgctatggttgctctgtt-ttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
                  |||   |  ||| || |  |     | ||   |       | | |     |   |   |||   | |  |  | ||| ||||||||| ||||||||||||||||| |||||||| ||||| |||||||||||||||||||||||||| ||||| || || || || || ||  | ||||||||
-----------------gtataactattctattatgatggcaatgatggatatgatgatgagatgcacatcattttaatccttttccttttaattttgcagGATTTTGGGACATGTACGATCCAGAGGGATATTCTCTGTGGTTCTGTGATTACAAATACAATGATGAGAACACAGTTTCCTTTGTTACGTTAAACAAGGT

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G28670.1 (Glycine max), 3'ss of exon 6
gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
              | |||||  |   ||| || |       |   | |   | |  |   | ||| |   ||    | ||| |     | ||| ||||||||| ||||||||||||||||| |||||||| ||||| |||||||||||||||||||||||||| |||||  | || || || || ||  | ||||||||
-----------gtatagctat--tcattctattatgatggcatggatatgagatgcatgtcattttaatcctccttttaaattt-----taattttgcagGATTTTGGGACATGTACGATCCAGAGGGATATTCTCTGTGGTTCTGTGATTACAAATACAATGATGAGAACTCAGTTTCCTTTGTTACATTAAACAAGGT

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G40330.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------------------gcctagttgataa-----gttgcta---tggttgctctgttttctacttctca--ttcttcaaggtttaaaactttgaagttcacaa-----tgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
                                                           |  ||  |||  |      |||| |   | |||  | ||  |  | | ||  |   | || ||   |  | |      |||| |||      |||||    |  | ||  ||||||||| ||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||| | |||||||| || || || || ||  ||||||||||
gtattgtttttgtggcccctcgggctcgttgttttacatgtttcctaaattaggaatatgattatatgactataatcattgcaaaattagttattatgaatcttgcctcaaagaattttaaaaaatatatatgacacagttgacatccttttgaatccactttttatcttgcagGATTTTGGGACATGTATGATCCCGAGGGATACTCTCTCTGGTTTTGTGATTACAAATACAATCAGGAGAATACTGTTTCTTTTGTGACATTGAACAAGGT

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S172_22V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------gcctagttgataagttgctatggttgctctgttttctactt----ctcattcttc-----aaggtttaaaactttgaagttcacaatgaatatgttca---tgattatgc-agGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
               ||   || | ||  | | |   ||| || |  ||||     | ||| |||      || || |  | | | |   |   | |      ||  |    ||| ||||| |||||||||||| |||| |||| | ||||| |  ||  | ||||||||||||||||| |||||||| |||||    ||| | ||||| ||  |||| |||||
gtacgtcttctaatgagcatatgatttaatttagagcctcagtctgatactgagcacccatgcttatggagaatgtcttgaccctcggcttgtgctaacgtggtggacgggttgaatatgccagGATTCTGGGAAATGTTCGATGCTGAGGGTTGGTCATTGTGGTTCTGTGATTACAAGTACAATGATGAGAACCAAGTCACTTTCGTGACCATGAATAAGGT

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaa-tatgttcatgattat-----gcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
       |  | |||   | | ||    | |  |   | |  |  |   ||| |  |   |  ||||  | | | | |||  ||  ||  || || |     |||||||||||||| |||| |||  | || || |||||| | ||||||||||||||||| ||||||||||||||    ||  | || || ||| |||| || ||
---gcactttttagtcattctagtc-tgcagagtcagagtgtt--tctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ14564 (Selaginella moellendorffii), 3'ss of exon 6
gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
                                    |||   |  |  ||| |   || |    |||||  |    ||    ||   ||    | ||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||||| ||||| || ||||| || ||  | ||||| ||  ||||||||||
-----------------------------------gtacaagtggtgtttcca---ttgatcgcttgaaaatgctgattttgat-cccaaatctttgcagGATTCTGGGAGATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

upper sequence: Vv12s0035g01130.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttca-tgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
                                    |||   |  |  ||| |   || |    |||||    |   ||| | || ||  |     ||||||||||||||||||||| || |||||||||||||| || |||||||| || ||||| ||||| || ||||| || ||  | ||||| ||  ||||||||||
-----------------------------------gtacaagtggtgtttcca---ttgatcgcttgaaa---atgctgattctgatctcttcccttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

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|110372574|gb|EC936754.1|EC936754
EST:     GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAG                         GATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
genomic: GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAGgtatctctct ... gattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
EST: gi|110359163|gb|EC920208.1|EC920208
EST:     GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAG                         GATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
genomic: GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAGgtatctctct ... gattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
EST: gi|110727691|gb|EE104738.1|EE104738
EST:     GAAACTCTACTCAAATACCAAGAACAATTTCCGTGAGGTTGCATTTAAAG                         GAT-CTGGGGA-ACTGTACGATCCCGAGGAATACTCTC
genomic: GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAGgtatctctct ... gattatgcagGATTCTGGG-ACA-TGTACGATCCCGAGGGATACTCTC
EST: gi|110698460|gb|EE075982.1|EE075982
EST:     GAGACTCTACTCAAATACCAAGACCAATTTCCATGAGGTTGCAATTAAAG                         GATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
genomic: GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAGgtatctctct ... gattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
EST: gi|161713862|gb|FC062558.1|FC062558
EST:     GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAG                         GATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
genomic: GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAGgtatctctct ... gattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
EST: gi|110699423|gb|EE076408.1|EE076408
EST:     GAGACTCTACTCAAATACCAAGACCAATTTCCATGAGGTTGCAATTAAAG                         GATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT
genomic: GAGACTCTACTCAAATACCAAGACCAATTTCCGTGAGGTTGCAATTAAAGgtatctctct ... gattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcaaggtttaaaactttgaagttcacaatgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT
          tttaaaactttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctagttgataagttgctatggttgctctgttttctacttctcattcttcaaggtttaaaactttgaagttcacaatgaatatgttcatgattatgcagGATTCTGGGACATGTACGATCCCGAGGGATACTCTCTTTGGTTCTGTGATTACAAATACAATGACGAGAATACCGTCTCATTCGTAACTCTGAACAAGGT

- - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaatg