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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaatatttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC

Basic information

species Vitis vinifera
transcript Vv15s0045g00310.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 1
aataatt-tgtgtccatgttttttttttatttctccttaagttttcttgttcaatt-tatcaactgtt--tatgataaaatatttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
| | ||  |   |   ||   | |  | ||    |  | | |||    |    ||  | |  | ||||  | || | | | | |  ||  |||    |   |||| |||| |||||  | ||||||||||||||  ||||||| || ||||||||||||||  |||| || ||||||  |||||| || | ||| || ||||| 
attgatcatagttttgtgcagtgtagtaataatgctgttactttggcagcgagatgatttgcattgttggtttgctgagaaactctatcactg----cgtgcagGTTACACGATGTTATCCACAGTGAGAAGCGCATATATCTTGTCTTTGAGTATCTGGATCTGGACCTAAAGAAGTTCATGGACTCTTGTCCAGAGTTTGCG

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 2
-aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaatatttgatttctgt-tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
 |   ||     |     |||  | | |  |  || |    || |  ||     ||  |||| |  ||||  | |  |  ||  |   ||| ||  ||||||| | |||||||||||||||||||||||||| || ||||| |||||||||||||||||||||||||| || || ||||||||||||||||| || ||||  
tagccatgaaaatgttactttgctatgtgctgttcttcgtcttattctgcctttttagtcaattcattat--tgagttgctttgtggttgtgtggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTATCTGGACTTGGATCTAAAAAAACACATGGATTCATCTCCAGAGTTTGTG

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 2
aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaatatttgatttctgt-tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
    ||     |     |||  | | |  |  || |    || |  ||     ||  |||| |  ||||      ||  ||| |   ||| ||  ||||||| | ||||||||||| |||||||||||||| || ||||| |||||||||||||||||||||||||| ||||| || |||||||||||||| || ||||  
ggccatgaaaatgttaatttgctgtgtgctgttcttcctcttattctgcctt-ttagtcaattcattattgagttatgcttggtggttgtgtggatgacagGTTGCAGGATGTAGTACACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTATCTGGACTTGGATCTAAAGAAACATATGGATTCATCTCCAGAGTTTGTG

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 1
----aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaatatttgatttctgt-tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
    ||| || |   | ||| |  ||  |  |||  |     | | || ||  ||  ||  |||  |  | || || |     ||| | | ||| ||     |||| | |||||||||||||||  ||||||| | || ||||| ||||||||||| || ||||| ||||| ||||||||||||||||||||||| || ||||| 
ctttaattatgttgcttcatttagttcatacattgttgtcctaatgttatttgtctcttagtcatttcctcattatca-----ttggtgtatgtgtggaacgcagGTTGCAGGATGTAGTGCACGATGAGAAGAGTTTGTATCTGGTTTTTGAGTACCTTGACTTAGATCTAAAGAAGCACATGGATTCATCTCCAGAATTTGCA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 2
aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgat---aaaatatttgatttctgt-tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
    | || |||   |   ||  |||  | | | | |   | | ||  |   |||||||   |  | ||      |  ||  ||| | | ||| ||    ||||| | ||||||||||| ||   ||||||| | || ||||| ||||||||||| || ||||| ||||| ||||||||||||||||||||||| || ||||| 
----aattatgttgcttgcttcatttagtctgtacattgttgtcctaatgttatttatctcttaatcatttcctcattatcgttggtgtatgtgtggagcacagGTTGCAGGATGTAGTACATGATGAGAAGAGTTTGTATCTGGTTTTTGAGTACCTTGACTTAGATCTAAAGAAGCACATGGATTCATCTCCAGAATTTGCA

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 3
aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaat-atttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
               | |  | ||  ||    |  | ||     ||  ||||   |    ||| |     | ||  |   ||||| | | |||    ||||  | |||||||| |||||||| ||||| || || ||||| |||||||||||||| ||||||||||| || ||||||||||||||  |||| |||||  ||
--------------gtatgatgttaataccattgttgaaaa---ctgattcagcatgatgactctggtaaacaattttgattgatgttttttgctacacagATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTGAGTATCTTGACTTGGATCTCAAAAAGCACATGGATTCTACTCCTGATTTCTCC

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S281_23V6.1 (Physcomitrella patens), 3'ss of exon 3
-aataatttgt-----gtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaatatttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
 |||| | |       ||||  ||  |   || |   |||    | | |  || |   |       | |    |   ||    || || |||           |||||| |||||||| || |||||||||||| | || |||||||| |||||||| |||||  ||||  | ||||| ||||||||  | | ||| ||| |||||
gaatattctcctgatagtccgagtcctggcttaagaactcaccgaatgtaattatgacaccacctgatttaccacc-tacgggatgtggttttgaccc-----cagGCTTCAGGATGTGGTACACAGTGAGAAGAGATTGTATCTAGTCTTTGAGTACCTGGATCTGGACTTAAAGAAACACATGGACACCTGTCCTGATCTTGCC

upper sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ15022 (Selaginella moellendorffii), 3'ss of exon 2
aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaatatttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
                                    |  || | |   | || | | |  | ||  | |  |||||    |   ||  | || |   |||  | || ||||| || ||  | ||||||  | | || || || |||||||| |||||||||||||| |||||||| |||||       || || || |||
-----------------------------------gtgcgtgtccacttccattctctggaatggat-ttctaaaacgaatcgattgggctgcc---cagATTGCAAGATGTGGTCCATTGCGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCC

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|30132539|gb|CB917878.1|CB917878
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|30128118|gb|CB913457.1|CB913457
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|110732023|gb|EE106947.1|EE106947
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|71875892|gb|DT024947.1|DT024947
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|30127193|gb|CB912532.1|CB912532
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|110716217|gb|EE091004.1|EE091004
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|29781538|gb|CB346072.2|CB346072
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|30126104|gb|CB911443.1|CB911443
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|161706121|gb|FC056257.1|FC056257
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|110702955|gb|EE079378.1|EE079378
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
EST: gi|30126370|gb|CB911709.1|CB911709
EST:     ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAG                         GCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA
genomic: ATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgtaggtcaca ... tgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcaatttatcaactgtttatgataaaatatttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC
                                atttgat  putative branch site (score: 5)
                                      tttctgtt  CT-rich tract
      aatttatcaactgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataatttgtgtccatgttttttttttatttctccttaagttttcttgttcaatttatcaactgtttatgataaaatatttgatttctgttgtctgacagGCTACAGGATGTAGTGCACAGTGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - ccatgtt
- - - - - - - - - - - - - - tttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaaa