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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattacttatttgctcaatttttttctattgtttgaaaagctatccgcataaaatggtggtcagaaggacttcctgtggtcttaggaataacagag...

Basic information

species Vitis vinifera
transcript Vv07s0130g00420.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os05g01060.1 (Oryza sativa), 5'ss of exon 18
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattacttatttgctcaatttttttctattgtttgaaaagctatccgcata---aaatggtggtcagaaggacttcctgtgg---tcttaggaataacagag
||||||||||   ||||| || |||||||||||||||||||| ||||||| ||| |   |||||| |||  |  | || || ||      ||||||   ||||||       | |   |   |||   | || ||||   || |    ||   ||   ||| ||||     |   | ||    |     | |||||  |       
GGAACCAGCTGTATTGGCAATAAAGAGGGAAGGTTACAGCATTAAGTGTAATGGCCAGCGTGGTGTTGTTATTACAGAAAAATTCCAGCAAGCCACTGCTgtatgtcctagaaatcattgtctttgaatttactgttctgaatgtatgccagttagaaaaagggtgcctttataaatttgtgatatatcttttaggtttg------

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os01g01800.1 (Oryza sativa), 5'ss of exon 18
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatg-----attacttatttgctcaatttttttctattg---tttgaaaagctatccgcataaaatggtggtcagaaggacttcctgtggtcttaggaataacagag
||||||||||| |||||| || ||||||||||| ||||| || || |||||||| |   |||||| |||  || | ||||| |||     ||| ||   |||| |     ||| | ||||   |     |   ||  |||   ||    |||     | |||   |   | || || |     |  ||    |||  | |        
GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGCTACAGTATTAAATGTACTGGTCAGCGTGGTGTTGTTCTCACAGAGAAATTTCAGCAAGCAACTTCTgtacgtccttattccgtattctttagcagtacatcatttgaatttcaggaagtagatctcattctaaaattgtgagcaaactctgttggttccttcagta--------

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G104377_T03 (Zea mays), 5'ss of exon 17
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattac-----ttatt-tgctcaatttttttctatt-gtttgaaaagctatccgcataaaatggtggtcagaaggacttcctgtggtcttaggaataacagag
||||||||||| |||||| || |||||||||||||||||| | ||||||| |||||   | ||||  || |||   ||||| |||     ||| |  |  |||||||| |     | ||| | |||||  ||| ||  || |||| | |   ||||  | |    | |      |||  |  || || | | |   |  |       
GGAACCAGCTATTTTGGCAATAAAGAGGGAAGGTTACAGCGTTAAGTGTAATGGACAGCGCGGTGTCGTTGTCATGGAGAAATTTCAGCAAGCGATGACCgtatgatttccaaaatcattgtcctcaaaatttctcagtttgtttaatactttatcttctttctttag------gaaaaatgtcttgggatttgtagcctcctttt-

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA20G35770.4 (Glycine max), 5'ss of exon 19
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattacttatttgct-caatttttttctattgtttgaaaagctatccgcataaaatggtggtcagaaggacttcctgtggtcttaggaataacagag---
||| ||||| || |||||||||| ||||||||||||||| ||||| || | |||||  ||||| | |||| || | || || |||||| |  |||| | |||| |||   |||||   |   ||| | |     | ||||   |  |   |    |   | |       |   |  | || |  |    | |||  |       
GGAGCCAGCCACATTGGCCATTACGAGGGAAGGTTACAGTATCAAATGCAGTGGACAAAGTGGAGTTGTAATCACAGAAAAATTTTCACCGTCCACCACTgtaagatgttttattctttgttattctgtatggatatttggctaatttatcattgattctaggaaatgaagtaaaattctttaat----gaaatgtccctttcc

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA10G31880.1 (Glycine max), 5'ss of exon 19
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattacttatttgctca-atttttttctattgtttgaa-aagctatccgcataaaatggtggtcagaag-gacttcctgtggtcttaggaataacagag
||||||||| || ||| ||||||||||||||||||| || ||||| || | |||||| | |||   |||| || | || || |||||| |  |||| | |||| |||   |||||   | | ||| | |     | ||||   ||  ||||        ||  |     |||  ||  |    |  | | | |||  | |   
GGAACCAGCGACATTGACCATTAAGAGGGAAGGTTATAGTATCAAATGCAGTGGACCAAATGGATTTGTAATCACAGAAAAATTTTCACCGTCCACCACTgtaagatgttttattcttttatattctgtatggatatttggctaatttatcattgattcatcattccaggaaatgaagtaaaattctttaatgaaatata---

upper sequence: Vv07s0130g00420.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT5G23490.1 (Arabidopsis thaliana), 5'ss of exon 18
------GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgatta----cttatttgct-caatttttttctattgtttgaaaagcta----tccgcataaaatg-gtggtcagaaggacttcctgtggtcttaggaa--taacagag-------------------------------------------------------------
      |||| |||| || ||  | |||||||| |||||||||||||||||||||| |      |||| |     | |  | || ||||| ||| || | || | |||| || |     |||||||| | |  |  |||| | |  |   | ||        ||    | ||| | ||||      ||   |   | |  ||| | |   | | ||||                                                             
TATATGGGAAGCAGCAACATTATCTATTAAGAGAGAAGGTTACAGCATCAAGTGTATT------AGTGATCTCACAATTGCAGAAAAGTTCTCAGCATCTACTACTgtaagacttatgccttatttgtttctgtccttttttgtcataaaataaatcgcgcttctctgtgaaacgtgtggcggtgtgggtatggagagagctttgcatgttgaaagagttattagataggttctgaactttgaactaatatttatatccgtcttgtgatacctatgtag

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|30130582|gb|CB915921.1|CB915921
EST:     CTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAAT                         GTTAGCATTCCTTATGGACATCCAGAAGAGTTCTTAGTTATTGGTTCTGGC
genomic: CTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattac ... ccttcttcagGTTAGCATTCCTTATGGACATCCAGAAGAGTTCTTAGTTATTGGTTCTGGC
EST: gi|110360360|gb|EC923401.1|EC923401
EST:     CTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCTACAAAT                         GTTAGCATTCCTTATGGACATCCAGAAGAGTTCTTAGTTATTGGTTCTGGC
genomic: CTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattac ... ccttcttcagGTTAGCATTCCTTATGGACATCCAGAAGAGTTCTTAGTTATTGGTTCTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGAAGTTTTCATCAGCCACAAATgtatgattacttatttgctcaatttttttctattgtttgaaaagctatccgcataaaatggtggtcagaaggacttcctgtggtcttaggaataacagag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaata