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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGAAGTCCTCCTTGGCCATCTCGACTGGACCCCTGTTCACAAAGATCCCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtatttttttctccttctgagttctttcttcgtggctttatcttctaaactgtgatgtcttcattgacagtgtgctctacatgcacaacatcgatgatat...

Basic information

species Vitis vinifera
transcript Vv16s0039g01610.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g01610.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os07g36470.1 (Oryza sativa), 5'ss of exon 6
ACAAGAAGTCCTCCTTGGCCATCTCGACTGGACCCCTGTTCACAAAGATCCCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtatttttttctccttctgagttct---ttcttcgtggctttatcttcta-aactgtgatgtcttcattgacagtgtgctctacatgcacaacatcgatgatat
 ||| |||| || ||||||||||| |||||| | ||  | |||||||| || |  |||||||| || ||||||| ||| |||||||| ||||||||||||||||  |||   | || |  | |      | |||    |  ||| || |  ||||    |      ||||    |    | | | ||| |    || | |    
GCAACAAGTTCTTCTTGGCCATCTTGACTGGTCTCCAATGCACAAAGACCCAAGTTTCTGGCGCGAGAACATTAATAATTTTGAAGAAAATGATTTCCAGgtatgctttgtcctttattggatgggaaatattccaatcaatattttatggaacttcagtaagactattggagattctttatgcttgcccttgttccagg----

upper sequence: Vv16s0039g01610.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G163233_T04 (Zea mays), 5'ss of exon 11
ACAAGAAGTCCTCCTTGGCCATCTCGACTGGACCCCTGTTCACAAAGATCCCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtatttttttctccttctgagttctttct-tcgtggctttatcttcta----------aactgtgatgt----cttcatt----gacagtgtgctc-tacatgcacaaca-tcgatgatat--------------------------------------------------------------------------
|||  |||| || ||||| ||||| |||||| | ||  | ||||||||||| |  ||||||||||| |||||||  || |||||||||||||||||||||||||   || | | ||||   ||    |  | |||  | || | |             || |||||| |    || | ||     ||  |||| || || ||   | |   | ||  ||                                                                            
ACAGCAAGTTCTTCTTGGTCATCTTGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttgccctttcttctttgggacaattgtgattatacccttcgctggtcttgcaattgtgattttaccctccgttttccaactttgtgttcatagataagctattctggacaattcaatgttatagattagataggctcacaagcatttagctctgtggttgtgatgaaattgcacttataacttggcag

upper sequence: Vv16s0039g01610.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G019999_T01 (Zea mays), 5'ss of exon 8
ACAAGAAGTCCTCCTTGGCCATCTCGACTGGACCCCTGTTCACAAAGATCCCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtatttttttctccttctgagttctttcttcgtggctttatcttctaaactgtgatgtcttcattgacagtgtg-ctct-acatgcacaacatcgatgatat
|||  |||| || ||||| ||||| |||||| | ||  | ||||||||||| |  ||||||||||| |||||||  || |||||||| |||||||||||||||    ||  |||||     ||  ||     |   |  ||   ||    ||     |     |    ||| |  |||| | || || | |   | |  |||
ACAGCAAGTTCTTCTTGGTCATCTGGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAAAATGATTTCCAGgtacaccttg-tcctttcatcttgattgaaaatatttaaataaacttg-ttgcacaattgggctaagtagtttaactctcaaattcatagctaagctattat

upper sequence: Vv16s0039g01610.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA02G06710.1 (Glycine max), 5'ss of exon 11
ACAAGAAGTCCTCCTTGGCCATCTCGACTGGACCCCTGTTCACAAAGATCCCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtatttttttctccttctgagttct-ttcttc-gtggctttatcttctaaactgtgatgtcttcattgacagtgtgctctacatgcacaacatcgatgatat
 |||||||| |||||||||||||| || ||| | ||  | |||||||||||||| |||||||| || || || |  ||||||||||| |||||||||||||||| | |   |  | |    || | | |||| |  |  || |    ||| |    |||   |  |||    || |    | |   |     ||  | |  |
GCAAGAAGTTCTCCTTGGCCATCTGGATTGGTCTCCCATGCACAAAGATCCCATATTCTGGCGAGAAAATATAAACAACTTTGAAGAAAATGATTTCCAGgtatctatgcattatcccttcttttatgcttcagccgaattcttgattaagcacacatgaaatttttgg--atgagaaaaataacaaggctttcagttactt

upper sequence: Vv16s0039g01610.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA16G25740.1 (Glycine max), 5'ss of exon 11
ACAAGAAGTCCTCCTTGGCCATCTCGACTGGACCCCTGTTCACAAAGATCCCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtattt-----ttttctccttctgagttctttcttcgtggctttatcttcta---aactgtgatgtcttcat-tgacagtgtgctctacatgcacaacatcgatgatat
 |||||||| |||||||||||||| || ||| | ||  | |||||||||||||| |||||||| || || || |  ||||||||||| |||||||||||||||| |     || |||| | || | |  |||||| ||   || || |  ||   || ||  || |||     ||| | || | |  || || | |  |          
GCAAGAAGTTCTCCTTGGCCATCTGGATTGGTCTCCCATGCACAAAGATCCCATATTCTGGCGAGAAAATATAAACAACTTTGAAGAAAATGATTTCCAGgtatctgtgcattatctcttccttactcttttctttgttatttcatgtaatataaaattggcatctctggggatgatattgggtttcacctggatagaaa---------

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|37188010|gb|CF607361.1|CF607361
EST:     CCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAG                         ATTCTTAGGGTCCTCATTACAATTTTGGACACGTCCAGTGACCCAAGGGCG
genomic: CCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtattttttt ... ttgcctgcagATTCTTAGGGTCCTCATTACAATTTTGGACACGTCCAGTGACCCAAGGGCG
EST: gi|110706801|gb|EE082646.1|EE082646
EST:     CCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAG                         ATTCTTAGGGTCCTCATTACAATTTTGGACACGTCCAGTGACCCAAGGGCG
genomic: CCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtattttttt ... ttgcctgcagATTCTTAGGGTCCTCATTACAATTTTGGACACGTCCAGTGACCCAAGGGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAAGAAGTCCTCCTTGGCCATCTCGACTGGACCCCTGTTCACAAAGATCCCATGTTCTGGCGTGATAACATTAGTAACTTTGAAGAGAATGATTTCCAGgtatttttttctccttctgagttctttcttcgtggctttatcttctaaactgtgatgtcttcattgacagtgtgctctacatgcacaacatcgatgatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc