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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG

Basic information

species Vitis vinifera
transcript Vv03s0038g02760.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 3
gtattcctcacttatttagtatttttatttattccttt-ctgattcatatgatttccatctgtt--cagaatctattgatcaatgattttctt-tctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
                  |||  |     | ||||| | |  |||   |  |     ||||| |  ||   | || ||| || |  |||  |  | ||| | |  ||||| || || || || || ||||| || || || ||||||||||| || ||||| ||||| ||||| || |||||||| ||||| || || |||||||||
------------------gtacgtgctactgttcctctacaaattttcaacagactaatctggtagcaagttatactgagcatttctttcttcatgtaacttcttcagGGCCCAAAGTACCAGGAAATTGTAAACATCCGATTGGGAGATGGCACCACTCGCCGTGGCCAAGTTCTGGAAGTTGACGGTGAAAAGGCTGTTGTGCAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
gtat-tcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcacc---agGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
|| | | |    || |  | |||  | ||   | || |   ||||   |  |  ||  |||| | ||  |||  || |   |   |||  ||  |  | || |   |||| || || || ||||| ||||| || || ||  | |||||||| || ||||| |||||||||||||| ||||||||||| || ||||| |||||||||
gtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgct-agcctcttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 2
------gtattc-ctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
      || | | |    || |  | |||  |  |   | || | | ||||   |  |  ||  |||| |       |||   ||  |   ||   |    ||  ||  |||| || || || ||||| ||||| || || ||  | |||||||| || | ||| |||||||||||||| ||||||||||| || ||||| |||||||||
gtaaaggtgtgcacagttttctccaatatgatgctaactaccctgcagattttgaacagctcattctgctagcctcttatacttcctttgcttgtgtatccat--cattagggcccaaagtaccaaGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 3
gtattcctcactta-tttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
|| | |     ||  |  | |||  |  |   | || | | ||||   |  |  ||  |||| |       |||   ||  |   ||   |    ||  ||  |||| || || || ||||| ||||| || || ||  | |||||||| || | ||| |||||||||||||| ||||||||||| || ||||| |||||||||
gtgtgcacagttttctccaatatgatgctaactaccctgcagattttgaacagctcattctgctagcctcttatacttcctttgcttgtgtatccat--cattagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 3
---gtattcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattga--tcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
    |  |  |    || ||  |||||||| | | |  |||||| |   |  | ||||    | ||| |     | | |  |  ||  |||    |  || |||| ||||||||||||| |||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||||| ||||| ||||| |||
gtaatgatggtgtgctagttgatatttttaatgaat--tttctggtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 4
------gtattcctcacttatttagtatttttatttattcctttctgattcatatgatttccat-ctgttcagaatctattgatca-atgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
       |  |   |   |   |  |||| ||||| | |  | |  | ||  |||  | || ||  | | | |   |||  | | | ||  | | ||    || |||| ||||||||||||| |||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||| ||||| |||||||| || || || ||||| |||
gtaatgatggtgtgccgcttgctgatattgttattgaattttctgggttttttattttctcaatgttctgctgtgactaaagtttatattttatactgataaactgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGCGAAAAGGCTGTTGTTCAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 3
--------------gtattcctcacttatttagtatttttatttattcctttctgattcatat-------gatttccatctgttcagaatctattgatcaa-tgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
              ||  | |||   | | |  |||  |||||      |||   | |  | |       |||  ||| || ||     | |  ||| | | |  | | ||    || | || |||||||| || | |||||||||||| |||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||||||||| || || ||||| |||
gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 3
--------------------------gtattcctcacttatttagtatttttatttattcctttctgattcat-atgatttccatctgttcagaat-ctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG-
                             ||  |  |||||    |||| | |  | | |   | |  |  || | |||  ||| || ||    ||  |||   | | |  | | ||    || |||| ||||||||||| | |||||||||||| || ||||| || |||||||| || ||||| ||||| ||||| ||||||||||||||||| || || ||||| ||| 
taacgagtgtagtgtaatactctatttgctttgttgcttatggcttattctaaagtttgcaacttttctcaatgaagatgaccaactattttttatgttatgactgagttttatgctgatcaactgcatcaggGACCCAAGTTTCAAGAGATTGTTAACATTCGCTTAGGAGATGGTACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAGG

upper sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
gtattcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
                  |||||  | |||    ||||||  || |||   ||  | ||   |  |  | |  |||| |   | |   || ||     | | |||| || ||||| ||||| ||||||||||| ||| | || |||||||| || |||||||||||||| || ||||||||||| |||||||| ||||| |||
------------------gtattggtgtttccatctttctcttttataatgttctcgtcccat--gggtttcctgatgat--actgctttcct-----ctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG

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|110730165|gb|EE106929.1|EE106929
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|71862417|gb|DT011472.1|DT011472
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|71861168|gb|DT010223.1|DT010223
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|56409259|gb|CX017511.1|CX017511
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|71864966|gb|DT014021.1|DT014021
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|71859980|gb|DT009035.1|DT009035
EST:     GCCATTGGTCATCCTTGAGAAAGTCGAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|110357277|gb|EC920703.1|EC920703
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|71861589|gb|DT010644.1|DT010644
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|56409525|gb|CX017777.1|CX017777
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
EST: gi|56409500|gb|CX017752.1|CX017752
EST:     GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAG                         GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT
genomic: GAACTGTCTCTGGAGTCGCTGGGCCATTGGTTATCCTTGAGAAAGTCAAGgtattcctca ... attgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttccatctgttcagaatctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG
                                        ttctaat  putative branch site (score: 2)
                                  ttttctttctaatt  CT-rich tract
                                 attttctttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT