Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtggaattgttacagttttaaaattgtcatgagcatatggatctctacaatccatgtaatatcaatttaatacaaaaggtttgctttaacaaatgtgttctttcatgatggtgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTCTCTCCTAAGAAGCCAACTACTCTGCCTGAGGTGGCCAAGCAGCGTGAGC

Basic information

species Vitis vinifera
transcript Vv18s0001g05480.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g05480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G11160.4 (Glycine max), 3'ss of exon 4
gtatatgtggaattgttacagttttaaaattgtcatgagcatatggatctctacaatccatgtaatatcaatttaatacaaaaggtttgctttaac-aaatgtgttctttcatgat----ggtgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTCTCTCCTAAGAAGCCAACTACTCTGCCTGAGGTGGCCAAGCAGCGTGAGC
                            |||   || || | |  |||   |  |   | | |  |||  ||   | |      ||    || | | |||| || | |||  || |    | |||||   |||||||   | ||| |||||| || ||||| |||||    || |||||||| ||||| || ||||| |||||| |||||||||||||||||||||||||||
--------------------------gtatttatataagaacaaagatgctttta---cctattgtattgatcatagatttgcagtggatttcagctaaatttgatttttgttgttcactgttgaattgaagCAAGCGATTTCTGGAATCAGCCATATCTCCTTTGGCGAGGAGGAGAGTGTTTCTCCAAAAAAGCCCACTACTTTGCCTGAGGTGGCCAAGCAGCGTGAGC

upper sequence: Vv18s0001g05480.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G10930.3 (Glycine max), 3'ss of exon 4
gtatatgtggaattgttacagttttaaaattgtcatgagcatatggatctctacaatccatgtaatatcaatttaatacaaaaggtttgctttaacaaatgtgttctttcatga-tggtgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTCTCTCCTAAGAAGCCAACTACTCTGCCTGAGGTGGCCAAGCAGCGTGAGC
                    || || | |     |  |  || |   | |  | | |  || | |||  |  ||  ||||   | |||    ||||     | ||  ||  | | || ||||    |||||||   | ||| |||||| || ||||||||||||   || |||| ||| ||||| || ||||| ||| || |||| ||||||||||||||||||||||
--------------------gtatttatacaagaactaagatgtt--tttacatattttat-tgataatagatt--tacagtggatttcagctaactttgatttttattgttcactgttgaaatgaagCAAGCGATTTCTGGAATCAGCCATATCTCATTTGGTGAGGAGGAGAATGTTTCTCCAAAAAAGCCCACTTCTTTGCCAGAGGTGGCCAAGCAGCGTGAGC
















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|351042370|gb|FQ442837.1|FQ442837
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|71871397|gb|DT020452.1|DT020452
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351055304|gb|FQ441902.1|FQ441902
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351025084|gb|FQ433501.1|FQ433501
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|349808206|gb|FQ403393.1|FQ403393
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|161715954|gb|FC065517.1|FC065517
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351052161|gb|FQ450731.1|FQ450731
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351033213|gb|FQ461985.1|FQ461985
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|352795622|gb|FQ480210.1|FQ480210
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351034181|gb|FQ463115.1|FQ463115
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351016411|gb|FQ423838.1|FQ423838
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351056465|gb|FQ454326.1|FQ454326
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|110703051|gb|EE079558.1|EE079558
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|110429233|gb|EC995723.1|EC995723
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351022504|gb|FQ447026.1|FQ447026
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|349824984|gb|FQ406556.1|FQ406556
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351022653|gb|FQ428562.1|FQ428562
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|110700659|gb|EE077505.1|EE077505
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351055621|gb|FQ452086.1|FQ452086
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|71867999|gb|DT017054.1|DT017054
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351038942|gb|FQ457617.1|FQ457617
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351034791|gb|FQ458148.1|FQ458148
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351036728|gb|FQ457441.1|FQ457441
EST:     GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
EST: gi|351052900|gb|FQ453887.1|FQ453887
EST:     GAAGTGCGAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAG                         CAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC
genomic: GAAGTGCAAACCCTACTCCTAATAACAAAACAACAGTACGCATTTACCAGgtatatgtgg ... tgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatacaaaaggtttgctttaacaaatgtgttctttcatgatggtgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTCTCTCCTAAGAAGCCAACTACTCTGCCTGAGGTGGCCAAGCAGCGTGAGC
                 ctttaac  putative branch site (score: 3)
                  tttaacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgtggaattgttacagttttaaaattgtcatgagcatatggatctctacaatccatgtaatatcaatttaatacaaaaggtttgctttaacaaatgtgttctttcatgatggtgaatgacagCAAGCAGCTGCTGCAATCAGTCAGATCTCATTTGGTACAGAAGAGAGTGTCTCTCCTAAGAAGCCAACTACTCTGCCTGAGGTGGCCAAGCAGCGTGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC