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

CGTGGAAATCAGGGAGGAAATCGGGGAGGAGAACTTTTTTCTCTTTGGTGCCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgtgatatccttatgttcagcaaaaaaaatatttgcttttgcattaaatgactcctgatactctgaatctttaggttcctataattggcagat...

Basic information

species Vitis vinifera
transcript Vv06s0004g06020.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06020.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA18G07480.1 (Glycine max), 5'ss of exon 13
CGTGGAAATCAGGGAGGAAATCGGGGAGGAGAACTTTTTTCTCTTTGGTGCCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgta-aaactgtgatatccttatgttcagcaaaaaaaatatttgcttttgcattaaatgactcctgatactctgaatcttt---aggttcctataattggcagat
 ||||||||||||||||| ||  | |||||||| ||||| || ||||||||||||||||| || ||||||    || | ||| || | |||  ||||||||||   | |   ||      |||||  || |  ||  ||||| |  |   || | | |  |  |  |  ||| | |||||   |      |  |||| |||   
TGTGGAAATCAGGGAGGAGATTAGTGAGGAGAATTTTTTCCTTTTTGGTGCCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAACGCGAGAATGGACTGgtatgcagttcaattgatgcatgttttgctaccaat-tattttccatgaaatgata-gcttttttcttttctaagtctttcaaaaagggttgcaatttgcaa--

upper sequence: Vv06s0004g06020.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA08G45210.1 (Glycine max), 5'ss of exon 14
CGTGGAAATCAGGGAGGAAATCGGGGAGGAGAACTTTTTTCTCTTTGGTGCCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgtgatatccttatgt-tcagcaaaaaaaatatttgcttttgcattaaatgactcctgatactctgaatctttaggttcctataattggcagat---
 ||||||||||||||||| || || ||||| || ||||| || ||||||||||||||||| || ||||||    || | ||| ||||||||  ||||||||||   | || |||||| |   | |      |  || ||||| |  ||  ||  |||  ||  |  | || |  |       |||   | |||  ||| |    
TGTGGAAATCAGGGAGGAGATTGGTGAGGATAATTTTTTCCTTTTTGGTGCCACAGCAGAAGATGTCCCTCGACTGAGGAAGGAAAGAGAGAATGGACTGgtatg-cagtaatatccatgcatgtttttccaccaattattttccattaaat--aatagcttttacttctttacaaaggctcgttaaaa-aatgtgcaaaaaca
















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|110405644|gb|EC971188.1|EC971188
EST:     CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|46917547|gb|CN546876.1|CN546876
EST:     CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|110703465|gb|EE080336.1|EE080336
EST:     CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|30251461|gb|CB969194.1|CB969194
EST:     CCACAGCGGAAGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGGATCCCCGGTTTGAAGNGGCCATGCAATTCA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAG-ATCCCCGGTTTGAAGAGGCCATGCAATTCA
EST: gi|30251459|gb|CB969192.1|CB969192
EST:     CCACAGCGGAAGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGGACTNGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|110701622|gb|EE079402.1|EE079402
EST:     CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGATAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTTGAA-AGGCCATGCAATTCATAAAAACTGG
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTT-GAAGAGGCCATGCAATTCATAAGAACTGG
EST: gi|110384669|gb|EC949123.1|EC949123
EST:     CCACAGCAGAAGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|28960619|gb|CB340317.1|CB340317
EST:     CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|37190441|gb|CF609790.1|CF609790
EST:     CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTG-A
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|30251485|gb|CB969218.1|CB969218
EST:     CCACAGCGGAAGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|30135822|gb|CB921160.1|CB921160
EST:     CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
EST: gi|28960453|gb|CB340229.1|CB340229
EST:     CCACAGCAGATGAAGTCCTTAAGTTGCGCAAGAAAAGAGAGGCTGGACTG                         TTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA
genomic: CCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgt ... tcccctacagTTCAAGCCAGATCCCCGGTTTGAAGAGGCCATGCAATTCATAAGAACTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGGAAATCAGGGAGGAAATCGGGGAGGAGAACTTTTTTCTCTTTGGTGCCACAGCAGATGAAGTCCCTAAGTTGCGCAAGAAAAGAGAGGCTGGACTGgtaaaactgtgatatccttatgttcagcaaaaaaaatatttgcttttgcattaaatgactcctgatactctgaatctttaggttcctataattggcagat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa