Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG

Basic information

species Vitis vinifera
transcript Vv00s0225g00090.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 6
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
          |||  | |  | ||||    || || ||||    |  | ||  |   ||   ||  ||  || |   | ||  |  |  ||    ||   || || ||          || |||| ||||| ||||| ||    || || |||||||| ||||||||||||||||| ||||||||  | || || || || |||  ||||||||| |||||||
---------attatgctt--ggtgatgaa-ttagttttaccgg-gccgatgacaagaatgtattttat--ggttgcacctataggctgattggacttaactttgttata--------atgtagGGATGTGACTGCTTGGGTGTCATAAAATACTTTGATGCACATTTTACAAATTTTACTGGTGGCGTAGAGACCATAGAGAATGCTGTTTGCTTACATGAAG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
                                     | ||      ||| |||   |||  |||| ||  |  | |  |||   |  | |   | || | ||    | | | |||     |||| ||||| || ||||| |  || ||||| ||||| ||||| || || ||||| || |||||| | ||||||||||| |||||||| || |||||||| |
------------------------------------gtgcttgctcagttcttaatgattttttacctccagagagttttaactttcatctgactattatatgcctttttttttgt-----agGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcat-gtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
                                        |||| |  |   |   |  |   || |    |    ||| |||  || |||  |||   | || || |   |  | | |||||||| || |||||||| || || || || || ||||| |||||||| ||||| |||||||||||| | || |||||||| || |||||||| |||||||| |
--------------------------------------gttattttattcagttcttgatgtgtatactttgacgttcaaaatttttctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
|| |  |   || || |||   |  | |       |||||| |  ||  |         ||  || || |  ||||    |||        || ||||  ||||| |  |     |  ||||||| |||||||| ||||| ||||||||||||||||| || || || ||||| || | ||| ||| | |||||||| || ||||||||||||||||||||||
gtcaaggcattttcttctaatttagtctc----aaattactctcctttct--------ctatgtagatgaaactaa----aat--------ttattttgcttggtgacat-----tattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 6
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
        |   |  | | |||| || |||  |  |||  | |  || || ||     ||  | |    | |   || | | ||| ||| ||||          | |||||  | |  | |||||||||||||| ||||| |||||||| |||||||| || ||||| ||||| |||  ||| ||| | |||||||||||||| |||||||| ||||| ||||
--------gtaaaggcatttgcttatattccattcattcttgtctttatttttcctcctttctca----atgtagatgaaattgaatttgttttgc-------ataatgtcattat--ttcagGGCTGTGATTGTTTAGGCTATATCAAATACTTTGATGCGCATTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAAAACTGTGTTTGTTTGCACGAAG

upper sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 6
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG-
                 ||     |||| |||  |||| |     || ||||  |   || |   | |    | |||   |||||  ||   ||| ||||    | ||||   |||  | |||||||| ||||| ||||| |||||||| |||||||| || || || ||||| |||  ||| ||| | ||||||||||| || |||||||| |||||||||| 
-----------------taaatgcatttgctt-atattccagacattcttgtcttcattttgcctcctttctc-aatgtaaatgaaattgaatttgttttgca-taatgtgactgt--ttcaggGCTGCGATTGTTTAGGCTATATCAAATACTTTGATGCGCACTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAGAACTGTGTTTGTTTGCATGAAGA

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|71862014|gb|DT011069.1|DT011069
EST:     TTGATGCTGGTGAAGATGGGCTGGGTAAAAATGCACATTCTCTAAAGAAG                         GGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAAT
genomic: TTGATGCTGGTGAAGATGGGCTGGGTAAAAATGCACATTCTCTAAAGAAGgttagagtgc ... tgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAAT
EST: gi|71872208|gb|DT021263.1|DT021263
EST:     TTGATGCTGGTGAAGATGGGCTGGGTAAAAATGCACATTCTCTTAAGAAG                         GGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAAT
genomic: TTGATGCTGGTGAAGATGGGCTGGGTAAAAATGCACATTCTCTAAAGAAGgttagagtgc ... tgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAAT
EST: gi|161718570|gb|FC065389.1|FC065389
EST:     TTGATGCTGGTGAAGATGGGCTGGGTAAAAATGCACATTCTCTTAAGAAG                         GGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAAT
genomic: TTGATGCTGGTGAAGATGGGCTGGGTAAAAATGCACATTCTCTAAAGAAGgttagagtgc ... tgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG
  ggctaat  putative branch site (score: 3)
     taatcataatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG