Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctctcctcttagatcagtatctccattttttcccttgattctagggttttgttcttgattgtactggttttgcag

Basic information

species Vitis vinifera
transcript Vv06s0004g06880.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os03g18180.1 (Oryza sativa), 5'ss of exon 1
CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaa------ttctctcctcttagatcagtatc--tccattttttccc---ttgattctagggttttgttcttgattgtactggttttgcag---
 ||||||||| |||||||| || |||||||| || ||||| |||||||| ||||| ||||||||||||||||||||||| || || | | | |||||  |||||      | | |  | ||     |||   |  |||  | |  |||   ||   |||  |  |     || | || |  ||| ||| | |   
GCGAGGACGAGGACACCGGCGCCCAGGTCGCGCCCATCGTCAAGCTCGAGGAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGAGGTCCTCCTCGACATgtaagccgcctccccctccctcgatccagccccgatccgatctcccccggctttgatctgagcctgacgactcgttttttttggatttcccgcag

upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os05g28290.1 (Oryza sativa), 5'ss of exon 1
CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctctcct-----cttagatcagtatctccattttttcccttgattctagggttt---tgttcttgattgtactggttttgcag-------------------------
 |||||| || ||||| || || |||||||| || |||||   |||||| ||||| ||||||||||||||||||||||| || ||||   | |||||  ||| |  | | ||      |   | |   | ||||   | ||  ||    |  |   | |    || | ||  | |    | | | |  |                         
GCGAGGAGGAGGACACGGGCGCCCAGGTCGCCCCCATCGTGCGGCTCGAGGAGGTCGCCGTCACCACCGGCGAGGAGGACGAGGACGTGCTCCTCGACATgtgagccccccccgccgccgccgcttgctctctctcctcttctcccctctcttgtagctcgtgtgctttttttcggttcgatctggtggcgctgatccgcgcgattgtttgcag

upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G111411_T02 (Zea mays), 5'ss of exon 1
CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaa--ttctctcctcttagatcagtatctccattttttcccttgattctagggttttgttcttgattgtactg------gttttgcag
  ||||| || ||||| || || ||||| ||||| |||||   ||| || ||||| ||||||||||||||||||||||| || |||| | | |||||  ||| |    | ||||      ||     | | ||||  | | |  | ||    |     | ||    | || |||      |||||||||
GGGAGGAGGAGGACACGGGCGCCCAGGTGGCTCCCATCGTGCGGCTTGAGGAGGTAGCCGTCACCACCGGCGAGGAGGACGAGGACGTCCTGCTCGACATgtgaggcgccctccctccccatgtacttgttcattgctgcgcgcggttggccgcccccgctcgatttagtgctgattcgggttttgcag

upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT5G58590.1 (Arabidopsis thaliana), 5'ss of exon 1
CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgta----attctctcctcttagatcagtatctccattttttcccttgattctagggttttgttcttgattgtactggttttgcag--------------------------------------------
 ||| || ||||||||||| || ||||| ||||||||||||| ||| ||||||||||| |||||||||||||| || |||||||||||||| |||||||||||    | ||  |||  | | ||     | ||| |   |    || |    || |||   || | ||| | |   |  |  | |                                            
ACGAAGATGAAGACACCGGAGCTCAGGTAGCTCCGATCGTTAGGCTTGAAGAGGTTGCAGTCACCACCGGCGAAGAAGATGAAGACGCCGTCCTCGATCTgtatgttactcgttccgttaatattctagtttccttgcctctggttaaagtgagtgttggattttcgatagaagatgagtgtcggatttttgatagaagatgtattcttctgggtttatgattttgtag

upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G07140.1 (Arabidopsis thaliana), 5'ss of exon 1
CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctctcctcttagatcagtatctccattttttcc---cttgattctagggttttgttcttgattgtactggttttgcag---------------------------------------
 |||||| || |||||||| || ||||||||||||||||||| ||| || |||||||||||||| ||||||||||| || ||||| ||||| || ||||||||| | | |  ||||| ||  || | |  | ||||||    || | |     || | || ||    || ||  ||||| ||                                         
ACGAGGATGAGGACACCGGAGCTCAGGTCGCTCCGATCGTTAGGCTTGAGGAGGTTGCCGTCACTACCGGCGAGGAAGACGAAGATGCCGTCCTTGATCTgtaagtgtttt-tctta-attggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataa-ggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaag

upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT2G30060.1 (Arabidopsis thaliana), 5'ss of exon 1
CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctctcctctta-----------------------gatcagtatctccattttttcccttgattctagggttttgttcttgattgta---ctggtt-ttgcag---------------
 ||| || ||||||||||| || ||||| ||||| ||||| | ||| ||||| || |||||||||||||| || || || |||||| || | |||||||||||  | |||||  |                         ||||  | ||   | |  ||||     ||||||| ||||  | | ||||       || || |||  |               
ACGAAGATGAAGACACCGGTGCTCAGGTTGCTCCTATCGTCAGGCTTGAAGAAGTCGCCGTCACCACCGGTGAAGAAGACGAAGACACCATCCTCGATCTgtatgtatctcccttcgtttaatctaattgcactggatctgatcgttttccgtagtagttcctcaagttctaggattttagtttcgattcggagcttgattgttgttgtgcgaaaatctgtag

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|110694049|gb|EE070825.1|EE070825
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110710444|gb|EE086786.1|EE086786
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|161707126|gb|FC056389.1|FC056389
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110686104|gb|EE063409.1|EE063409
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110689315|gb|EE065434.1|EE065434
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|37183761|gb|CF603115.1|CF603115
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|294966177|gb|GW839400.1|GW839400
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|37184112|gb|CF603466.1|CF603466
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110723271|gb|EE100389.1|EE100389
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110724975|gb|EE101275.1|EE101275
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110726623|gb|EE102567.1|EE102567
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|161709260|gb|FC057984.1|FC057984
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110732314|gb|EE107490.1|EE107490
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110687654|gb|EE065310.1|EE065310
EST:     CGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: CGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110687655|gb|EE065311.1|EE065311
EST:     CGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: CGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110372303|gb|EC936456.1|EC936456
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
EST: gi|110721265|gb|EE098063.1|EE098063
EST:     GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCATTCTCGATCT                         GAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG
genomic: GAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctct ... ggttttgcagGAAAGCGAAGCTTTACAGATTCGACAAGGATGGGAATCAATGGAAGGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGAGGACGAAGACACCGGGGCACAGGTCGCTCCGATCGTTAAGCTCGAAGAGGTTGCCGTCACCACCGGCGAGGAGGATGAAGACGCCGTTCTCGATCTgtaattctctcctcttagatcagtatctccattttttcccttgattctagggttttgttcttgattgtactggttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA