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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC

Basic information

species Vitis vinifera
transcript Vv05s0020g01890.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 3
agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgct--tctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
    | |||| ||| || |     |||  |    | |  || || | |      | |   || |  ||| ||| |  |||  || || |||| |    | ||||||| ||||| || || || |||||| | ||||| || ||  | |||||||| ||||||||||| |||||||| |||||||| ||||| ||||| ||||
caactgtgtttaatgttatgtactttta-gtcaaaacgtatattaacattttccttctcatgatattctgttgtt-ttaattatgtttttttatccttttagGTGGAACAGCTGCATAAAATTTTTAAGTTGTGTGGTTCCCCCACAGAAGAATATTGGAAAAAATCGAAGTTGCCTCATGCAACTATATTCAAGCCCCAAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 2
agggtttgttga-attttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaa---aattttcttttgtgtgctc-agGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
   |||  |  |  |  | | | |  ||   |   | | |||       |||  |||    || ||| ||   |  | ||   |||  || | |||    |  ||||||| ||||| || || || |||||||| || ||||| ||  | |||||||| |||||||| || ||| | || |||||||| ||||||||||||||||
---gttcatgcacgtaatgttgttcattccagccaatctaatga-atgccaattgtatttatg-ttccatgtttatttaatttaataatcatctgtcccttttagGTGGAACAGCTGCATAAAATTTTTAAGCTGTGCGGCTCCCCCACAGAAGAATATTGGAAAAAGTCCAAGCTACCTCATGCAACAATATTTAAGCCTCAAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 3
agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttcta----ttgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
    ||     | |||  |||||  |       | | ||||||| |     |   |  |||     |     || ||  |    |||   | ||      ||||||||| ||||| || || || ||||||||||||||||||||  |||||||||| |||||||||||||||||||| |||||||| ||||||||||||||||
----ttcagacagtttagtaggtcatatgttcagtcacaatttttattttcggtcattgctttccatgatattttctttttttgattgggtgtttgtctttcagGTGGAACAGCTGCATAAAATTTTTAAGCTATGTGGCTCTCCGACTGAAGAATATTGGAAAAAATCAAAGTTGCCCCATGCAACTATATTTAAGCCTCAAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 3
agggtttgttgaattttctaggtgtttgtggtggacc-caattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgc-----tcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
           | ||   |    || | || | |  | || |||| ||        |    |   | |  |  | | |    |||  || |||||         ||||||| ||||| || || || ||||||||||||||||||||  | |||||||| |||||||||||||||||||| |||||||| ||||||||||| ||||
------cagacatttcagtgatggtctatgtttgttcacagtttttaatttcatcaattcttttctatgatatttccatttgtttgattgtgtgtctgtcttctagGTGGAACAGCTGCATAAAATTTTTAAGCTATGTGGCTCTCCGACAGAAGAATATTGGAAAAAATCAAAGTTGCCTCATGCAACTATATTTAAGCCCCAAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
----agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
       |  |  ||   ||| |||       |  | | |  |||||  |  |||       |   || || ||    ||   |  | |    | | ||| |||||||| ||| | |||||||| || ||||||||||| || |||||||| || |||||||| || || || ||||| || ||||| ||||| || |||||||
cttggatgaatagtgcgctttttagtctgccatatttg-cttaatttgaatgcaactactttgtctctactgttaaaactggga--tgtacactatttgc-cagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 3
agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaa--aaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
   |||||| | ||||     |||  |    |  | ||   |    | |||  | |    |  | |   |    || |   | || | | |  |    | ||||||| |||||||| || || |||||| | |||||||| ||  | |||||||| |||||||| || ||| | || ||||| || |||||||||||||| |
-ccgtttgt-gcatttctgttgtgcatactatccaacccgatgaatagcaactgcatttatcttccatatttcactgatctagttatgtctactccttttagGTGGAACAGCTACATAAAATTTTTAAGTTGTGTGGCTCCCCAACAGAAGAATATTGGAAAAAGTCGAAGCTACCTCATGCTACAATATTTAAGCCTCAGC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------------agggtttgttga--attttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
                                                                                       ||  |||||||   ||   ||     |||   |   ||   ||| |||||   | |    |  | || || | ||   |  |   | ||| |||||  | ||||||||||||||||||||||||| || |||||||| ||||||||||| ||||| |||||||| ||||||||||| ||||| ||||| |||||||| ||||
gtaatctatgatggatacattatatagggtctatagttgcatcttttaagggcataatgtgtattcagtttactagtctaaggtgcaagattttgttgtccatggcctctcaattttctgct-acttgattgtgaaatttgtgctttg--gattttacttctataattagcatccttatgtgttgt-agGTGGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGATGAATATTGGAAAAAGTCAAAGTTGCCTCATGCTACCATTTTTAAGCCCCAAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------------------agggtttgttg--aat--tttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgct-cagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
                                                                                                ||| |||||||   ||   ||||   | ||| || |  ||   ||| |||||   |  | |  | | || || ||||  |||  |   || ||| |||| |  |||| |||||||||||||||||||| || |||||||| ||||||||||| ||||| |||||||| ||||||||||| ||||| ||||| |||||||| ||||
gtaatctctatgatggatacactatatagggcttaatgtctatagttgcatcttttaagggcttaatgtgtattcagtttactagtctaaggtgcaaggttttgttgtcgatggcttctcaat-tttctgct--acttgattgtgaaatttg--tgcttcagattttactgcta-taattagcatcctttatgtgttatagGTAGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGACGAATATTGGAAAAAGTCAAAGTTGCCACATGCTACCATTTTTAAGCCCCAAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------agggtttgttgaattttctaggtgtttgtggtggacccaatt-ttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtg-tgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
                                               | | | | || | ||| || |    | |||   ||     ||  |      |||       |||||||  |   | | | |  | ||   |||| | | ||||||||||||||||| |||||||||||||| ||||| ||||||||||| || || |||||||||| ||||||||| ||||| ||||| |||||||| | | 
gtaatctttaaatgattaatttcattttataatttctctaagagcataagatgtattcactttacttgtcaatggtgcaagattttgttgctcgtgttagaaggtttgtgcttctgatttggttgatatatatccactgtgcttcacagGTGGAGCAGCTACATAAGATATTTAAGCTTTGTGGTTCTCCTTCTGACGAGTATTGGAAAAAATTAAAGTTGCCACATGCTACCATTTTTAAGCCCCGAA

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------agggtttgttgaattttctaggtgtttgtggtggacccaatt-ttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtg-tgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
                                                                   |   | | |  | ||| || |    | |||   ||     ||  |      | |       |||||||  |   | | | |  | ||   |||| | |  ||||||||||||| || |||||||||||||| ||||| ||||||||||| ||||| ||||| |||||||||||||| ||||| ||||| |||||||| | ||
gtaatctctaaatgattaatttcattttataatttctctacgggcatctttcaagtttcaagagcataaaatatatccactttacttgtccgtggtgcaagattttgttgctcgtgttaaaaggtttttgcttctgatttggttgatatatatccactgtgcttcatagGTGGAGCAGCTTCATAAGATATTTAAGCTTTGTGGTTCTCCTTCTGATGAATATTGGAAGAAATCAAAGTTGCCACATGCTACCATTTTTAAGCCCCGAC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ35595 (Selaginella moellendorffii), 3'ss of exon 2
agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
                     || |    | |||      ||||   |     ||  ||   |  ||     |         ||  | |||   |  |||||||||||  |||||||||| ||||||||||||||||| || || ||||| || ||||||||||| ||  | || || || || || |||||||| || |
---------------------gtatgctcgttggtttttgttttacgat----gtttagtaacgcctgccttt--------cttcttattgatcgaacagGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC

upper sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ24328 (Selaginella moellendorffii), 3'ss of exon 4
agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
                     || |      |||     |||||   |     ||  ||   |  ||              |||  | |||   |  |||||||||||  |||||||||| ||||||||||||||||| || || ||||| || ||||||||||| ||  | || || || || || |||||||| || |
---------------------gtatgctccttggtttttattttacgat----gtttagtaacgcctgcc-----------tttcttattgatcgaacagGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC

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|30126701|gb|CB912040.1|CB912040
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|71873708|gb|DT022763.1|DT022763
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|110689805|gb|EE066351.1|EE066351
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|110726282|gb|EE101925.1|EE101925
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|34544526|gb|CF512758.1|CF512758
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|71871637|gb|DT020692.1|DT020692
EST:     TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: TTCTAGCTGAGTTATTGGCCGGGAAGCCTATCATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
EST: gi|77586479|gb|DV222360.1|DV222360
EST:     CATGCCTGGTCGCACCGAG                         GTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA
genomic: CATGCCTGGTCGCACCGAGgtaacttcaa ... gtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC
                           tgctaaa  putative branch site (score: 2)
                                    ttttcttttgt  putative PPT
                              taaaaattttcttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agggtttgttgaattttctaggtgtttgtggtggacccaattttgaaacaagagtacagctgcttctattgctgctaaaaattttcttttgtgtgctcagGTGGAGCAGCTACACAAGATATTTAAGCTATGTGGCTCTCCTTCTGAAGAATACTGGAAAAAATCAAAGTTGCCGCATGCAACCATATTTAAGCCTCAAC

-gggtttg
- - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - -gacccaa
- - - - - - - - - - - - - - - - - - - - - - gaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaaa