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

gtacctcatttttccccggactggtaatggagttgtacgtttttttttttttttttgatcgtgtaatttagggtttaaatttcatttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g05480.t01
intron # 1
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 1
lower sequence: GLYMA04G11160.4 (Glycine max), 3'ss of exon 2
----------------------gtacctcatttttccccggactggtaatggagttgtacgtttttttttttttttttgatcgtgtaatttagggtttaaatttcatttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAG
                       |   |  ||| | |   |  |  |  |    ||  |  | | | |  ||| ||||  |  | |  |||  || | | |||      ||  | ||| || ||||||||||| |||||||||||||| || ||||| || ||||||||||  |||   ||    |||||
gtacagtcctctgtttctgtttttcttttgtttcttctttgggtaatttttatttttcatttatctgtggtttgtttttttttttttttttttggctgatattgtggaatttca-gCCGTCGGATGGGATCAGGAAGGTGGTGTTTGGTGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAAAG

upper sequence: Vv18s0001g05480.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G10930.3 (Glycine max), 3'ss of exon 2
-----------------gtacctcatttttccccggactggtaatggagttgtacgtttttttttttttttttgatcgtgtaatttagggtttaaatttcatttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAG
                 ||  ||  | |||    ||  |  |  |   ||  |      |||| |||   | |  |    |  |||   | | | |||      ||  | ||| || ||||||||||| |||||||| ||||| || ||||| || ||||||||||  |||   ||    ||| |
gtctagtgtagtctactgtttcttttctttttttggtttcttctttaggtgattttaaattttatttacctgttttttcttctttttttgctgatattgtggaatttca-gCCGTCGGATGGGATCAGGAAGGTGGTATTTGGGGGTCAGGTCACCGATGAAGAGGTCGAGAGCTTAAATAAACG
















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:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|71871397|gb|DT020452.1|DT020452
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351055304|gb|FQ441902.1|FQ441902
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351025084|gb|FQ433501.1|FQ433501
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|349808206|gb|FQ403393.1|FQ403393
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|161715954|gb|FC065517.1|FC065517
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351052161|gb|FQ450731.1|FQ450731
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351033213|gb|FQ461985.1|FQ461985
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGGTGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|352795622|gb|FQ480210.1|FQ480210
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351034181|gb|FQ463115.1|FQ463115
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351016411|gb|FQ423838.1|FQ423838
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|161717140|gb|FC066563.1|FC066563
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351056465|gb|FQ454326.1|FQ454326
EST:     CCGCCGATGCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|110703051|gb|EE079558.1|EE079558
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|161706465|gb|FC057590.1|FC057590
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|110429233|gb|EC995723.1|EC995723
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351022504|gb|FQ447026.1|FQ447026
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|349824984|gb|FQ406556.1|FQ406556
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACCGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351022653|gb|FQ428562.1|FQ428562
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|110700659|gb|EE077505.1|EE077505
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351055621|gb|FQ452086.1|FQ452086
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|71867999|gb|DT017054.1|DT017054
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351038942|gb|FQ457617.1|FQ457617
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351034791|gb|FQ458148.1|FQ458148
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGGCTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351036728|gb|FQ457441.1|FQ457441
EST:     CTGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
EST: gi|351052900|gb|FQ453887.1|FQ453887
EST:     CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAG                         CCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA
genomic: CCGCCGATTCTCCCGCCTCCGCTTCTCGCCCTGCCGTCCGCTCTCACCAGgtacctcatt ... tttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttttttttttgatcgtgtaatttagggtttaaatttcatttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAG
             ttttgat  putative branch site (score: 4)
                                        tttcattttt  putative PPT
                                  tttaaatttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctcatttttccccggactggtaatggagttgtacgtttttttttttttttttgatcgtgtaatttagggtttaaatttcatttttggaagCCTTCCGATGGGATCAGTAAGGTGGTGTTTGGAGGACAGGTGACTGATGAAGAGGCGGAGGCTTTGTCGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG