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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACCCAGAATTGTCATTGTGGATGTGGACGATTACCGGTTATCTGTTGCAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatatttccatcttaaaaaattctattcattgcatcagtaaataatctgcttcaaattcctttcaatctacag

Basic information

species Vitis vinifera
transcript Vv16s0100g00300.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00300.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G27310.1 (Glycine max), 5'ss of exon 4
AGCACCCAGAATTGTCATTGTGGATGTGGACGATTACCGGTTATCTGTTGCAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgt-tctaatatttcca-tcttaaaaaattctattcattgcatcagtaaataatctgctt-caaattcctttcaatctacag-------------------
 |||||||| | ||||||||||||||| || || || || ||||||||||||||    |||||||| ||||| ||||||||||| || ||||| |||||||| | ||  ||    | | |   ||| |  |    |||   |   | || |||  || |    |    |  || ||| ||                    
GGCACCCAGGACTGTCATTGTGGATGTAGATGACTATCGTTTATCTGTTGCAAAATCACTTGGTGCCGATGACATTGTTAAAGTCTCAACAAACATTCAGgtatttagaatccttagtttcccaaagtcttccatattttcttctttaacaataagcatgttgaacaatcccattctgcaacactatttgcatctgtcat

upper sequence: Vv16s0100g00300.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G32360.3 (Glycine max), 5'ss of exon 3
AGCACCCAGAATTGTCATTGTGGATGTGGACGATTACCGGTTATCTGTTGCAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgt-tctaatatttccatcttaaaaaattctattcattgcatcagtaaataatctgctt-caaattcctttcaatctacag--------------------
 ||||||| ||  |||||||||||||| || ||  | || ||||||||||||||   ||||||||||||||| ||| ||||||| || ||||| ||| |||| | ||  ||    |  ||  ||  |  |    |||   |   | || |||  ||           |  || ||| ||                     
GGCACCCAAAACAGTCATTGTGGATGTTGATGACCATCGTTTATCTGTTGCAAAATCTCTTGGTGCAGATGATATTATTAAAGTCTCAACAAACATTAAGgtatttagaatccttagtttccaaggtcttccatattttcttctttaacaataagcaagttggacaatcccattctgcaacactatttgcatctgtcatt
















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|349823554|gb|FQ414964.1|FQ414964
EST:     CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAATG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|110407824|gb|EC973441.1|EC973441
EST:     CAAAGGAACTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|83276223|gb|DV940231.1|DV940231
EST:     CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|110718284|gb|EE094941.1|EE094941
EST:     CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTCCGACAAATATTCAG                         GATGTAGCTGAAGAAATGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|110732129|gb|EE107144.1|EE107144
EST:     CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|27581705|gb|CB004400.1|CB004400
EST:     CAA-GGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGC
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGC
EST: gi|110408106|gb|EC973729.1|EC973729
EST:     CAAAGGAACTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|110713228|gb|EE088964.1|EE088964
EST:     CAAAG-ATCTTGGTGCAAATGANATTGTTAAAGTTTCNACAAATATTCAG                         GATGTANCTGAAAAAGTGGTGCAAATACACAAAGCTATGGGACCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|110370270|gb|EC929261.1|EC929261
EST:     CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|110361632|gb|EC925120.1|EC925120
EST:     CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
EST: gi|26267678|gb|CA818741.1|CA818741
EST:     CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAG                         GATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG
genomic: CAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatat ... caatctacagGATGTAGCTGAAGAAGTGGTGCAGATACATAAAGCTATGGGAGCTAGAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCACCCAGAATTGTCATTGTGGATGTGGACGATTACCGGTTATCTGTTGCAAAGGATCTTGGTGCAGATGAGATTGTTAAAGTTTCGACAAATATTCAGgttctaatatttccatcttaaaaaattctattcattgcatcagtaaataatctgcttcaaattcctttcaatctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG