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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG

Basic information

species Vitis vinifera
transcript Vv05s0020g01780.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttatt--gcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
                  | | | |||||    |   |||  |      |  || ||  ||||   ||  |    | | |  |||||  |   |  ||||| || ||||| ||| ||||||| ||||||||||| ||| | |||||||||||||||||||||||||| ||||| |||||||| |||
-----------------gtatgtccttttcaaatcgtaattttttc---tcattctacaatttgtgaagttaaaggttatggttatttggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
    | ||      || |     |  ||||||| |  |   |    ||||   ||| ||   ||   |    ||| || | || ||  |  |  ||||| || |||| |||| ||||||| ||||| ||||| ||| |||| ||||| ||||||||||||||||| || ||||| ||||| |||
----gtatgctgttatgtgcaaattgttttcttctgaa---cccatgaatatgtatgttgaatatttagt--gttaatgtgttgatgtcttc--agGAATCCACAAGCTGATCTGCAAGCTCAAGACCGTGCACATAGGATAGGTCAGAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
--gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
   |||| | |   | |   ||  |||| || |||     |  ||| | |||   | || |   |           || | | | | |  | ||  ||||| || |||| |||| ||||||| || || ||||| ||| |||| |||||||||||||||||||||||||| || || ||||| |||
gtatgag-actatgctaaacttgattctgttgctt-----accctaag-aatgaatctaatgcct----------ctgttatttctgtgcctcc--agGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
gtgagc-atttctccatttttttttctttttcttttagaatgctagggaattgttatattatttacca-atctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
||  || | ||    ||  |   ||   |||  ||    || |     ||   | |    ||  |||  || |   |  |   | | |  | ||  ||||| ||||||| |||| ||||||| || || ||||| ||| | || |||||||||||||||||||||||||| || || ||||| |||
gtatgcgactttgttatgctaaatttagttttgttgcttataccct--aagcatgaagccatgaaccttatgttcctagtacttctgtgcctcc--agGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgt---tatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
|| || |||  |   ||  || |       ||| ||   |||   |      |   |  || | | |    | | ||||||   |       |    |||||||| ||||||||  ||||||| || |||||||||||| |||||||||||||||||||||||||||| || ||||| ||||| |||
gttagtattctt--gttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgt---tatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
|  || |||  |  |||  || |       ||| ||   |||   ||     |   |  || | | |    | | ||||||   |       |    |||||||| ||||||||  ||||||| || |||||||||||| |||||||||||||||||||||||||||| || ||||| ||||| |||
gcaagtattcat--attgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
|| || |||||      || |   ||    | | |    |      | |     ||  | |||    ||  ||||| |   ||||   ||     ||||||| |||||||| ||||| || || |||||||||||| |||||||||||||||||||||||||||| || ||||| || || |||
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattat-tttgttgat--ggttggtgcttttacaaca-----gGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
|| || ||||||     ||||   |     | | |    |      | |     | |||||||       |||||| |   ||||   ||     ||||||| |||||||| ||||| || || |||||||||||| |||||||||||||||||||||||||||| || || || || || |||
gtcagtatttctagtagttttgaacacagccatgttatttatatctgtacc--caaattattttgttga-tggttggtgcttttacaaca-----gGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattattt-accaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
              | | | |  || || ||   |  | |    |    || |  |    ||| || | |||||   ||              | |||||||| ||||| || |||||||| || |||||||| ||| ||||||||||||| ||||||||||||||||||||||||||||| |||
-----------gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctg----------gcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
              |    | ||| | | ||  ||  |||    | |   |||| | || | | || |    | ||      |||| |||     ||||||| |||||||| |||||||| || |||||||| ||| ||||||||||||| ||||||||||||||||| || |||||||| |||
------------gtaaggctctttttgtgtccattgtaatttatgag---tgttttcttttatgcctaatgaggtgggtggattatggca-----gGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctcttta-ttgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
                                             | |||  | ||  | | | |  |   |  || | |    | ||   | | ||||| || ||||| ||||||||||| |||||||| || ||||||||||| || || |||||||||||||| || ||||| |||||  ||
---------------------------------------------gtaataataatgatttgttctgagtggcatgtttttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
                                             | ||| || ||  | | | |  |   |  || | |    |||   | | ||||| || ||||| ||||||||||| |||||||| || ||||||||||| || || |||||||||||||| || ||||| |||||  ||
---------------------------------------------gtaatagtaatgatttgttctgagtggcatgttttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

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|29781883|gb|CB346697.2|CB346697
EST:     GGTATCAATCTTGCTACTGCAGATGTTGTCATCCTTTATGACAGTGACTG                         GAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCA
genomic: GGTATCAATCTTGCTACTGCAGATGTTGTCATCCTTTATGACAGTGACTGgtgagcattt ... tgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
                              ggttgat  putative branch site (score: 5)
                                    tctctttatt  CT-rich tract
      aattgttatattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT