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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgatctatttttttttcctaaatgaatttttatatagtttctttagttctgcttcctaataattctgctctattcagGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT

Basic information

species Vitis vinifera
transcript Vv06s0004g06860.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 16
----------------------------------gtcgatctattttt-ttttcctaaatgaatttttatatagtttctttagttctgcttcctaataatt-ctgctctattc------agGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
                                    |  |  |||    | || || | ||  || || ||   ||| |   ||| || | |  | || || ||| |  | |       |||||||||| |||||  |||| || |  |||||||| || ||||| ||  | |||||||||||||| ||||| ||||||||||| ||| |||| ||||| |
gttagcagttttttcccaataagttcggccttttacctttgcattgccatgttgctcagtggcttcttttacc-tttatactgttgtgttgctcagtagtttctgtttgaattgattgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 16
----------------------------------gtcgatctatt-tttttttcctaaatgaatttttatatagtttc-----tttagttctgcttcctaataatt-ctgctctattc------agGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
                                  | |  |  |||    | || || | ||  || || ||   ||       | |  || || | |  | || || ||| |  | |       |||||||||| |||||  |||| || |  |||||||| || ||||| ||  | |||||||||||||| ||||| ||||||||||| ||| |||| ||||| |
gttagcagttttttcccaataagttaggccttttgcctttgcattgccatgttgctcagtggcttcttttacctttatactgttgtgtttgtgttgctcagtagtttctgtttgaattggttgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 8
gtcgatctatttttttttcctaaatgaatttttatatagtttctttagttctgcttcctaataattctgctctattcagGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT-----------------------------------
                                                                               |     |||||||   || || | || || ||||| || ||||| ||  | |||||||||||||| ||||| ||||||||||| |||||||| ||||| |                                   
----------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngcggatgaaatcagcttgatt-cgttcccgaatgttgctgatgccattcttgctaatggtatgttcagTCATTATGATCGCCCTCGTATTGCTCAGCTGTGTGAAAAGGCTGGGTTGTACTTGCGAGCCCTCCAG

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
---gtcgatctatttttttttcctaaatgaatttttatatagtttcttta----gttctgcttcctaataa-ttctgctctattc-------agGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
        |  ||| ||  || | | |||||  |||   |     ||  |    | |   || |  |||   |||||||    |        |||||||||| |||||  | || || |  |||||||| |||||||| ||  | || ||||||||||| ||||| ||||| || || |||||||| |||||||
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 16
----------------gtcgatctatttttttttcctaaatgaatttttatatagtttctttagttctgcttc-----ctaataattc-tgctctattc--agGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
                ||     ||| | | |  |  || |||||       |  | | ||||| | |  |||       |||  | | || | ||||   ||||| ||||||| ||||| || || ||||||||||| || ||||||||||| || ||||| ||||| ||||| ||||||||||||||||||| ||| || |
gttctttttattttctgtgccattatctctgtccctgaactgaatcagatggtgatatatttagatttttttcaaatctcaattttccatgttttatttttagGTTCTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTCAGTCATTATGATCGCCCACGTATTGGACAACTAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 16
---------------gtcgatctatttttttttcctaaatgaatttttatatagtttctttagttctgcttcctaataattc---tgctctattc--agGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
               ||     ||| | | |  |  ||    ||  | ||||| ||   ||  || |   |  | | ||||    || | | ||   ||||| ||||||| ||||| || || ||||||||||| || ||||||||||| || ||||| ||||| ||||| |||||| |||||||||||| ||| || |
gttcttttattttctgtgccattatctctgtccctgaaccagatagtgatatatttagattttttttttataattacaatttccatgttttgtttttagGTTCTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTCAGTCATTATGATTGCCCACGTATTGGACAACTAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
gtcgatctatttttttttcctaaatgaatttttatatagtttctttagttctg----cttcctaataat-tctgctctattcagGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
||   | |||||| ||| | | |||   | |  ||  |     |   ||| |      ||  |  |||| | | || | || ||||  ||||||| ||||| || || ||||||||||| || ||||||||||| || ||||| ||||||||||| ||||| || ||||| ||||| ||||| |
gttcttttattttctttgctttaatctgtatccatgaaacaattggtgttatatagttttttttttaatatttactatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 14
--------------gtcgatctatttttttttcctaaatgaat---ttttatatagtttc-tttagttct---gcttcctaataattctgctctattcagGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
               | | | || | | | | | | |   |||   | |||||||||||  ||| ||| |     ||  | | |  | | || | || ||||  ||||||| ||||| || || ||||||||||| || ||||||||||| || ||||| ||||||||||| ||||| || ||||| ||||| ||||| |
gttctcttactttctttgctgtaatctctatccatgagccaattggtgttatatagttttgttttgtttttatatttttttaaatatttactatttttagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatttttatatagtttctttagttctgcttcctaataattctgctctattcagGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT
                               tcctaat  putative branch site (score: 2)
                                        ttctgctct  putative PPT
     ttttatatagtttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcgatctatttttttttcctaaatgaatttttatatagtttctttagttctgcttcctaataattctgctctattcagGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC