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

gtagtaaagttcagtgtttatcttcttgttcttccgtctgatcattgctgttgtcattattatcattatcatcagcaatattattattatcattatcaacattattattgttggtgctagaacttatatcaccatttttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG

Basic information

species Vitis vinifera
transcript Vv09s0002g02530.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G20930.2 (Glycine max), 3'ss of exon 12
gtagtaaagttcagtgtttatcttcttgttcttccgtctgatcattgctgttgtcattattatcattatcatcagcaatatta-ttattatcattatcaacattattattgttggtgctagaa-cttatatcaccatttttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG
                                                        |  || |   |       ||||||||  || |  || |  || || |  | ||   |  |  | ||| || || |    ||||   ||  ||||||||||||||| ||||||||||| |||||| |  || |||| ||||| | ||||||||||||||| ||||||||||| ||||||||||||
-------------------------------------------------------gtagttgtt-ctgcaggatgcaatattggttttcttcctcctctacttcctcatatatactaatggaagctaattttttaatttcaatcccagGTTCAAACATGCCTTGTACCCCTGAGGCAGTTCAGATTCTGAGGAAAGCTAGTGTTCTCATTGCTCCTGCAATGGCTGCCGGTGCTGGAGGG

upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G01510.2 (Glycine max), 3'ss of exon 12
gtagtaaagttcagtgtttatcttcttgttcttccgtctgatcattgctgttgtcattattatcattatcatcagcaatattattattatcattatcaacattattattgttggtgctagaacttatatcaccatttttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG
                                                        |  || |  || |     |||||||| |  || |  |  ||  | | ||   |  |  ||    | ||    |    ||||   ||  ||||||||||||||| ||||||||||| |||||| |  || | || ||||| | ||||||||||||||| ||||||||||| ||||||||||||
-------------------------------------------------------gtagttgttcttgtaggatgcaatattttggtttttttcctcttcctcatatatactaatg--gaagctacctttttaatttgaatcccagGTTCAAACATGCCTTGTACCCCTGAGGCAGTTCAGATTCTTAGGAAAGCTAGTGTTCTCATTGCTCCTGCAATGGCTGCCGGTGCTGGAGGG

upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G32870.1 (Glycine max), 3'ss of exon 3
gtagtaaagttcagtgtttatcttcttgttcttccgtctgatcattgctgttgtcattattatcattatcatcagcaatattattattatcattatcaacattattattgttggtgctagaacttatatcaccatttttc-tcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG-----
                      || | |||  | |   |  || |     | ||      |||  |      ||  | | ||  | || || |  |   | |  | ||   |  |  | |||  ||  |    |||||   ||  ||||||||||||||| | ||||||||| | |||| |  || |||| ||||| | ||||||||| |||||  |||||||||| ||||||||||||     
--------------------gtttttggttaattcaggttgtcgt-atactagtagaaggtattgtaggatgcaatattgtttattttttcctccttttcttcctcatatatacttatggaagctacttgtttattttgaatcacagGTTCAAACATGCCTTTTACCCCTGAGGGAGTTCAGATTCTGAGGAAAGCCAGTGTTCTCATCGCTCCTTCAATGGCTGCCGGTGCTGGAGGGATGAG

upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G28010.1 (Glycine max), 3'ss of exon 3
gtagtaaagttcagtgtttatcttcttgttcttccgtctgatcattgctgttgtcattattatcattatcatcagcaatatta-ttattatcattatcaacattattattgttggtgctagaacttatatcacca-tttttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG
                                                        |   | |  || |     ||||||||  || || || |  ||  | |  ||||   |  |  | |||  ||  |    | |||   ||  ||||||||||||||| | ||||||||| |||||| |  || |||| ||||| | ||||||||||||| | ||||||||||| ||          
-------------------------------------------------------gtagctgttcttgtaggatgcaatattggtttttttcctcctcttcttccttatatatacttatggaagctacttgtttagtttgaatcacagGTTCAAACATGCCTTTTACCCCTGAGGCAGTTCAGATTCTGAGGAAAGCTAGTGTTCTCATTGCTTCTGCAATGGCTGCCGGG---------

upper sequence: Vv09s0002g02530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G51720.1 (Arabidopsis thaliana), 3'ss of exon 12
gtagtaaagttcagtgtttatcttcttgttcttccgtctgatcattgctgttgtcattattatcattatcatcagcaatattattattatcattatcaacattattattgttggtgctagaacttatatcaccatttttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG
                  ||     || || |  |     |  ||| | |      |  || |  |  | |   |  |  || ||  | |  ||       || |||   |   | |||       |||     |||||     ||||||||||||||| |||||  |||||||||| |||||||| ||||| ||||||||||| |||||||| || || |||||||| |||||||| 
-----------------gtagagatttcttatatcaagcaactatttcagggcctctcgtt-ttgtgtttac--gttaggtttttgctgttctt-------ttgttacctt--atcctaag--cagtatggatgttttttgtgcagGTTCAAACATGCCGTGTACAGCTGAAGCAGTCGATGTTTTCAGAAAGGCGAATGTTCTGATTGCTCCTGCCATTGCTGCTGGAGCTGGAGGA

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|110374522|gb|EC939340.1|EC939340
EST:     ATCTGATGCCATAAATTTGGTAAATTCAGGTTGCCGGATACTAATAGAAG                         GTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGA
genomic: ATCTGATGCCATAAATTTGGTAAATTCAGGTTGCCGGATACTAATAGAAGgtagtaaagt ... tttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatcaacattattattgttggtgctagaacttatatcaccatttttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG
                                     tcaccatttttctctt  CT-rich tract
      aacattattattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtaaagttcagtgtttatcttcttgttcttccgtctgatcattgctgttgtcattattatcattatcatcagcaatattattattatcattatcaacattattattgttggtgctagaacttatatcaccatttttctcttagGTTCAAACATGCCCTGTACCCCTGAAGCAGTTGATGTTTTGAGAAAAGCGAATGTTCTCATTGCTCCAGCAATGGCTGCTGGTGCTGGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG