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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttctattctttctcaatgtcactgacacaacattggcccttgtacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 16
gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttctat--tctttctcaatgtcactgacacaacattggcccttgtacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT
                                                                            ||        |||  | |||    |   ||  |||  ||||  | |||    |||       ||  || | |  ||    || | |||||||||||||||| ||||| |||||||| ||||| ||  | ||||| ||||| || ||  ||  |    | || | |  | |  ||   | |  |||||| ||
---------------------------------------------------------------------------gtaaaccagaatttaatgttt---gtgcttagtaatggctatgatgttttgtgatgaattgaccatgacttagttcca---actctttacagATATGAAAGGAAAAATAAGAGTTTTTTGTCGCTTGCGCCCTCTAAGCGACAAGGAACTTTCTTTTGAGGAGAAAAATATAGTTTGCAGTCCTGATGAATT

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 16
gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttctattctttctcaatgtcactgacacaacattggcccttgtacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT
                                                                      || ||  |   |     || ||  ||        |||    |   ||  ||||| |       |||  ||  |||     |   || | |||||||||||||||| ||||| |||||||| ||||| ||  | ||||| ||||| || ||  ||  |    | || | |  | |  ||   | |  |||||| ||
----------------------------------------------------------------------gtaaaccagaataaatgtttgtgcttag------taatggctatgatattttctga-------tgaaccatgatttattttccaactctttacagATATGAAAGGAAAAATAAGAGTTTTTTGTCGCTTGCGCCCTCTAAGCGACAAGGAACTTTCTTTTGAGGAGAAAAATATAGTTTGCAGTCCTGATGAATT

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 21
gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttc--tattctttctcaatg-tcactgacacaacattggcccttgtacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT
                                                                |   |  | |||  | ||  | |||||  |      | | | |   | |    ||  | | | | || ||||  |  |||| ||||  |||||     || |||| ||||| ||||| |||||||||| ||||||  |||| |||||||| ||||||||| |||||||||||||||||   ||||||| | |  ||||||| ||
---------------------------------------------------------------gtggatgatcaaaactctttatttttggaatccagtctatgtgaatgtgttgacatcatatataactggtcacatattcaaccttggaacttgtttttctttcagACATGAAGGGCAAGATCAGAGTTTACTGTCGACTAAGACCTCTTAGTGAAAAAGAGATTGTTGAGAAAGAAAGAGAAGTTCTTACTGCAGTTGATGAATT

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 18
gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttctattctttctcaatgtcactgacacaacattggcccttgtacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT
                                                    |   |  |  |  || ||  |||   |||||   |   |||| | |  | | |    |  |  || | |     ||  |||  |  |||| ||||  ||||      || |||| ||||| ||||| |||||||||| ||||||  |||| |||||||| ||||||||| ||| |||||||||||||   ||||||| | |   |||||||||
---------------------------------------------------gtgggtgattgaaactctt--taa---ttttggaatcaagtctatga-gtatgtgttgacatacatacataactgat--cacatattcaaccttggaacttggttttctttcagACATGAAGGGCAAGATCAGAGTTTACTGTCGACTAAGACCTCTTAGTGAAAAAGAGATTGCTGAGAAAGAAAGAGAAGTTCTTACTGCCACTGATGAGTT

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 18
gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttctattctttctcaatgtcactgacacaacattggcccttg--tacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT
                                                ||  |  ||    |||  || |   | | || || |   || ||       || | ||   ||||  ||    | | | || ||     || |||||||    ||  |    ||| |||||||||||||||| || |||||||  ||||||||||| |||||||| ||||||||| |||     |||||||||  |  ||||| ||||  |||||||||
------------------------------------------------gtggtggatagaatatatttatacaagaaatattatgtatttgt-----gaatgtgtag--atttacata---tataactgacataataactacattggattatggttcttaatttcagATATGAAAGGCAAGATAAGAGTTTATTGTCGGTTAAGACCTCTTAGTGAAAAAGAGATTGCAAGCAAAGAAAGAGATTCTCTTACTACTACTGATGAGTT

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 18
gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttctattctttctcaatgtcactgacacaaca------ttggcccttg--tacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT
                                                                |  |      ||| | ||  |    |   | | |  | |||  |||||| ||   || |  | | | ||||||| || |      ||||    ||  |    ||| |||||||||||||||| || |||||||  ||||||||||| |||||||| ||||||||| |||     |||||||||  |  ||||| |||| | ||||||||
---------------------------------------------------------------gtggtggacagaatttatttataccagaaatattatgtatctgtgaatttgtagatttacata-tataactgacataataactacgttggattatgattctttatttcagATATGAAAGGCAAGATAAGAGTTTATTGTCGGTTAAGACCTCTTAGTGAAAAAGAGATTGCAAGCAAAGAAAGAGATTCTCTTACTACTGTAGATGAGTT

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|351015272|gb|FQ445556.1|FQ445556
EST:     TTACAAGGACGAACAAGTTCTAAGGAAGCGATATTTTAACATAATAGAAG                         ATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAA
genomic: TTACAAGGACGAACAAGTTCTAAGGAAGCGATATTTTAACATAATAGAAGgttggcattg ... cacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAA
EST: gi|351043062|gb|FQ443904.1|FQ443904
EST:     TTACAAGGACGAACAAGTTCTAAGGAAGCGATATTTTAACATAATAGAAG                         ATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAA
genomic: TTACAAGGACGAACAAGTTCTAAGGAAGCGATATTTTAACATAATAGAAGgttggcattg ... cacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAA
EST: gi|351026499|gb|FQ428511.1|FQ428511
EST:     TTACAAGGACGAACAAGTTCTAAGGAAGCGATATTTTAACATAATAGAAG                         ATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAA
genomic: TTACAAGGACGAACAAGTTCTAAGGAAGCGATATTTTAACATAATAGAAGgttggcattg ... cacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctattctttctcaatgtcactgacacaacattggcccttgtacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT
                    cactgac  putative branch site (score: 2)
     attcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcattgccttaaagtttttaatatatttaatgatattcttttaggtcatatatcttctattcttttgttaaatattttgttctttggtctttcacatctctaagaatttctattctttctcaatgtcactgacacaacattggcccttgtacacattacagATATGAAAGGCAAAATCAGAGTTTTCTGTCGGTTAAGGCCTCTTAGCGAAAAAGAGGTTGTTGAGAAAGAAAGATGTGTTCTTAATACTTTTGATGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG