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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgcatgtgttcctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaattgtgaacttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG

Basic information

species Vitis vinifera
transcript Vv08s0007g08690.t01
intron # 1
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 2
-----------tgcatgcatgtgtt-cctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaattgtgaacttaac-atcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG
           |  |||| | | |    |||| | ||| |     || |  || || |   |     | || ||||  ||  || ||   ||     |||||  |   | ||||||||| ||||||||||| ||| |  | ||| |||||||||||||||||||  | ||||| |||||||| ||||  || || || || || || || |||
gtatccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacg--tacaagagtttctatcctt--ttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g24220.3 (Oryza sativa), 3'ss of exon 1
-----------tgcatgcatgtgtt-cctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaattgtgaacttaac-atcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG
           |  |||| | | |    |||| | ||| |     || |  || || |   |     | || ||||  ||  || ||   ||     |||||  |   | ||||||||| ||||||||||| ||| |  | ||| |||||||||||||||||||  | ||||| |                                      
gtatccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacg--tacaagagtttctatcctt--ttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACG--------------------------------------

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G180988_T02 (Zea mays), 3'ss of exon 2
---------------tgcatgcatgtgttcctgttattgttctagatattgaacaagctgct--attgtcttaa--ttgctatttt------tgcttctggaattgtgaa-----cttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG
               |   |   | | |||   || |  ||  ||| | |||   |  |  |  |||  || ||  |||| | | |      || || || |  | |        |||| |||  | |||||| || ||||||||| | |||||  | ||| ||||||||||  ||||||| || ||||||||||||||||||   || || || ||||| || ||||||
gtatcctttcacatgtttgtcagtatattctgcttctcttttaagaaactgatagattttttccatttactcaagcttgcaaatatagaacatgtttatgaatgtatatgtatcccttagcataatttagTGGGACAGAAATATGGCGGATTGAAGATTTTAAGCCAGTTCCGCTGCCAAAATCTGATTATGGTAAATTCTACTGTGGAGATTCATACATAGTTCTGCAG

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G21350.1 (Glycine max), 3'ss of exon 1
-tgcatgcatgtgttcctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaa-ttgtgaacttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG
 || |||  | | |  ||   |||  |    ||||||    |  |  |    | || | |    | | |||||   ||  || | |||||||| |  ||||| || || ||||||||||| |||||||| |||||||||||| | ||||| || || || ||||| ||||||||||| || || || |||||  || |||||
atggatgattttatgtctagcattcatgct-atattgtgttatatattga-atattgaatatactgtatgctttgagaggttttaaacttaacttgctgtagAGGAACTGAAATATGGAGGATTGAGAATTTTCAGCCAGTTGCATTGCCCAAATCTGAGTATGGCAAATTCTACACGGGAGATTCGTACATCATCTTGCAG

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 2
--------tgcatgcatgtgttcctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaattgtgaacttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG
           || ||  | |     |||||||||||| |||         |  |||    |  ||   | | | | |||  ||| || |  ||||| | | |||||| ||||| ||||||||||| |||||| | |||||||||||||| ||||| |  || || ||||| ||||||||||  || || ||||||||  || |||||
atgtaattgatattcaaatataagcattattgttctagttat-------attattataagttggatatat-tatctacttgaggagttttagacttagctttttgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 1
tgcatgcatgtgttcctgttattgttctagatattgaacaagctg--ctattgtc--ttaattgctatttttgcttctggaattgtgaacttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG
   ||| |  || |  |   ||| |   |  |||||  | || |    |||| |   || | |    | | | |||  ||| || |  ||||||| | |||||| || || ||||||||||| |||||| | |||||||||||||| ||||| |   | |||||||| ||||||||||  || || ||||||||  || |||||
---atgtaattgatattcaaatt-taagaattattgttctagttatattattataagttgaatatattatctacttgaggagttttagacttaactttttgtagAGGGACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGACCTGATTATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgtcttaattgctatttttgcttctggaattgtgaacttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG
                                     gaacttaac  putative branch site 
        ttaattgctattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatgcatgtgttcctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaattgtgaacttaacatcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-gcatgca
- - - - - - ttcctgt
- - - - - - - - - - - - - - - - - -gaacaag
- - - - - - - - - - - - - - - - - - - - - ctgctat