Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA

Basic information

species Vitis vinifera
transcript Vv04s0008g04280.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 2
-taaaagcttaacttgttctc-ctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
 | ||   |     | |   |  ||  ||  |||  ||   ||   ||       |   |    || |||  |     | |    |       || |  |||  | || | |||  | ||  |||||||||||||  ||||||| ||||||||||| |||||||| |||||||| |||||||| ||||| ||||  || || 
ctgaagcatctgtgtatgagcattgcaaggaacactattgtttagattgttatttacacatgttcacaatgtt--gctatttaaagacaaatgccttttcagGATTAATGCTCTTTTTGACCACTTCAAGATGGCCTTGGATTGTTTCTTTGCTGTGTGGTTTGTCGTAGGAAATGTGTGGATATTTGGCGGGCGTTCTTCT

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
----taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
    || ||| || |     ||   ||  |    |    |   ||    |||  || |  |  |  |||  |  | | | |  |     || | | | |   ||  |  | |   |||| |  | ||||||  ||||||||||||| ||||||||||| |||||||| || || || |||||||| || || || |   | || 
atactagaagattcaaca--tcatatgaaaccatctgagttctttcttctaactaacatttggattcat--ttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G089466_T01 (Zea mays), 3'ss of exon 2
------------------------------------------taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
                                          |  |   | ||  ||||   |||| | ||      | | || |         |||  |   | ||   | | |||  | | |   |   ||  ||| |||  | || |  ||| | ||  ||||||||||||| |||||||| |||||||| || |||||||| || |||||||||||||| ||||| || |  || || 
gtactcatgccttctttttttccttaaaaaaatggatcggtatttacaatgaatatgtttgactgtcacttgttttgtttatttatggtgctgcaaa--atggctatg-cattaaagatgaatgccctgtgctatctg-cagGATCAATGCGCTGTTTGACCACTTCAAGATGGCCCTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTTGGAAACGTGTGGATATTTGGTGGCCGTTCTTCT

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G092244_T03 (Zea mays), 3'ss of exon 2
--taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
  ||      | | ||| |  |    ||  || |     || | ||    | ||| |||        ||   ||         |  ||   |||  ||   | |  ||| || || || |  ||||||||||||| ||||| |||||||| ||||| |||||||| || ||||| |||||| | ||||| || || || || 
cctactgttctcatttgatagcagcatacctatacag-gtcatcagaatcataaatactttgttggcaagttttctctgagctgcattctcctcgttgtagGGCCCAAGCTTTTGCTG-ATCACTTCAAGATGGCGCTGGACTGCTTCTTCGCTGTATGGTTTGTTGTGGGAAATGTGTGGGTGTTTGGTGGACATTCTTCC

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
--taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccc-tggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
  | | |  ||||  | || |    | | ||| ||  | ||  |  ||  | | |    | | |      |  |    ||    ||||  |||  |    |||| | |||   || |||||||||||||| ||  || | |||||||| |||||||| |||||||| || ||||| || ||||||||||| || || || || 
tttgatattttaatgtattgtttcatga-ttataactt-tcaagtattgga-atatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
--taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
      || ||      ||   |  | | | |  |  |    ||| ||||     || || |   || | | ||    ||   |  | |   |   |  |||| | ||| | || |||||||||||||| || ||| | |||||||| |||||| | |||||||| || ||||| || ||||| |||||||| || || || 
agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaata-acttatga-agttgctaagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------------taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagta----ggtgtttg--tctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
                                                                                            | | || |||  |   |||  ||||   || |   | ||||    |  | || | || ||| |  | |   | || |  |    |||  |||  | |  ||  |||||| || ||| | |||||||||||||| ||||||||||||||||||||||| || |||||||||||||| || || ||||| ||||||||||| || || 
gtaaacacacatgttcttagatgatctgtttcaactgaaagtttggattttgaattacgttttctctcaaagcttttcttatttttgagaattgagagtttagatgtctcttttgtt--ctaaactttttctttgtgttgaaaatatctgcaatctaattgagtcagtatgattttggtcgttgattttggcttccagACTTAAAGTTATCGTGGAATACTTCAAAATGGCTCTGGATTGCTTCTTTGCGGTGTGGTTTGTGGTAGGTAATGTATGGATATTTGGAGGGCATTCATCT

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ36853 (Selaginella moellendorffii), 3'ss of exon 1
taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA---------
                               | | |   |    ||   |      |   |   |  |   ||  |         |  |||      |||  |       ||||||||  | |||||||| ||  ||||||||||||| || || ||||| || || || ||||||||||| ||||| || ||||||||          
-----------------------------gtatggtgcttc--cttttgctgtcttttttatacttttctctattgttcttcgactaatctattcatcagtgttggaagGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCGTCCCGCGAA

upper sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ27808 (Selaginella moellendorffii), 3'ss of exon 1
---------taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatact---taaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
          |    | |   ||   |   ||  | || |  | |||  ||  |                  ||| |  |   ||  |         |  |||      |||  |       ||||||||  | |||||||| ||  ||||||||||||| || || ||||| || || || ||||||||||| ||||| || |||||||| 
gtcgcgaggaagggacgtggattccgcgagtgacaatt-cggggtatggtgcttccttttgctttcttttttatatttttctctattgttcttcgactaatctattcatcagTGTTGGAAGGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCG

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|161720218|gb|FC070870.1|FC070870
EST:     TCTGTTCCAGCCACAAGAAACAGTCAAAGTGTAAGGAGATTAAGTGCAAG                         ACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGC
genomic: TCTGTTCCAGCCACGAGAAACAGTCAAAGTGTAAGGAGATTAAGTGCAAGgtatgaattt ... tccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA
                                       tttgtctccct  CT-rich tract
                  ataatacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
taaaagc
- - - - - - - - -ctcctgt
- - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaggtg