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

GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaatgatgctttcaatgttgactagctgttagatgtgacattgaagatccaaatcctatcaataaccatttc...

Basic information

species Vitis vinifera
transcript Vv01s0011g03380.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 5
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttga--tgctcaaatgatgctttcaat-gttgactagctgttagatgtgacattgaa-gatccaaatcctatcaataaccatttc
|| |  || ||||| || ||||| ||||| ||||| || ||  ||||||||||||| ||||| ||||| || || ||||||||||| ||||    |    |  |  |  |  |||    || ||   |||   ||| |      |   | ||      |  | | |    |   |||||||  |    
GGAGGCATAATGGCTGTCGGAGCCTCAAAACCTACAGTGGTGGCTGATAAAGATGGTTTCTTTAGTGTCAAGAGCAAAATGCTGgttagttgcccttcacacatgcaatttttcagccaatactggaaattagtgattgttatattagtatgttgggaagtgcttctgtgctcctcaataaaaa----

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G121200_T01 (Zea mays), 5'ss of exon 5
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaat--gatgctttcaatgttgactagctgttagatgtgacattgaagatccaaatcctatcaataaccatttc-
|||||||||||||| |||||||| ||||  |||||||| ||  ||||||| ||||| ||||| ||| | || ||| |||||||||| ||||||||   |||| |  || || ||||  ||   |  | | | |  || | |  |   ||     | | |  ||       ||    |||   |    
GGGGCTATCATGGCTGTTGGAGCGTCAAGACCTACTGTAGTGGCTGATAAGGATGGTTTCTTTAGTATCAAGAGTGAAATGCTGgttagtttattctcgtatctgtat-ctaaaatttgagtataccgaagct--ctggttactgactgatgtttagtatttctggcatttacatgtaattgtgaag

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 5
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaatgatgctttcaatgttgactagctgttagatgtgacattgaagatccaaatcctatcaataaccatttc-
|| ||||| ||||| |||||||| || || ||||| |||||  ||||||||||||| ||||| || || || || ||||||||||| ||||   | |   ||| | ||   ||  || |  || || | |    || | ||  | ||  |  || |   |   | | |||      |||| ||  
GGAGCTATTATGGCTGTTGGAGCCTCGAAACCTACAGTTGTGGCTGATAAAGATGGTTTCTTTAGCGTCAAGAGCAAAATGCTGgttagttgtgtacctgattgtaatagacatctgttatttgca-tataatgtatcagtatggtgaaatgtttatagttttacttctacatcctaccaatttt

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 5
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaatgatgctttcaatgttgactagctgttagatgtgacattgaagatccaaatcctatca-ataaccatttc
|| ||||| ||||| |||||||| || || ||||| |||||  ||||||||||||| ||||| || || || || ||||||||||| ||||   | |   ||| |  |   ||   | || || || | | |  |  | ||  | ||  | |||||   | | | |  || |   ||   |||| 
GGAGCTATTATGGCTGTTGGAGCCTCGAAACCTACAGTTGTGGCTGATAAAGATGGTTTCTTTAGCGTCAAGAGCAAAATGCTGgttagttgtgtacctgattgttttagacatccgttggttgca-tatagcatttcagtatggtgaaatattgatagttctacttgtacctcgtactgatttt

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G24830.2 (Glycine max), 5'ss of exon 5
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaatgatgctttcaatgttgactagctgttagatgtgacattgaagatccaaatcctatcaataaccatttc---
|| ||||||||||| ||||| || ||||||||||||||| |  |||||||||||||||||||||| || || | |||||||||||||||||  ||    ||  ||    ||    | ||   ||   ||   |   ||| |||||    |     |  || ||  |     ||    |  |||    
GGTGCTATCATGGCTGTTGGCGCATCAAAGCCTACTGTTCTGGCTGATAAAGATGGATTCTTCAGCGTGAAGAATAAAATGCTGgtgagttacttgtcatagcttataactacttttatttgtttg-tgcacatatgct-ttaga-acaatggacagaattcaggtgaatacagactcttttttgtg

upper sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G25860.1 (Arabidopsis thaliana), 5'ss of exon 5
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaatgatgctttcaatg-------ttgact----agctgttagatgtgac--attgaagatccaa---atcctatcaataaccatttc---------------------
|| ||||| ||||| |||||||| |||||||| ||||| ||  ||||||| ||||||||||||||||| ||||  | ||||||||| |||||  || ||  ||   |  ||    |||||  ||   ||       | ||||    |  | | | ||  ||     |  || |       || ||| || ||||  | ||                     
GGTGCTATTATGGCTGTTGGAGCGTCAAAGCCAACTGTAGTTGCTGATAAGGATGGATTCTTCAGTGTAAAAAACACAATGCTGgtaagttttattttgacttaataaacttcc-tgatgggtttggtgaatcacttcgacttagaaagtttaaaatacgattagctatagcttttggctatgctaacagtaacattgtcgctttgttgttatgttggcag

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|27582046|gb|CB004741.1|CB004741
EST:     ATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: ATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|29785993|gb|CB343386.2|CB343386
EST:     CTGTTGTCACTGATAAAGATGGATTTTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATTTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|77587425|gb|DV222856.1|DV222856
EST:     CACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|110399056|gb|EC965543.1|EC965543
EST:     CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|26259444|gb|CA810507.1|CA810507
EST:     CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
EST: gi|77583069|gb|DV220571.1|DV220571
EST:     CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTG                         GTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC
genomic: CTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttat ... cctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGCTATCATGGCCGTTGGAGCTTCAAAGCCTACTGTTGTCACTGATAAAGATGGATTCTTCAGTGTTAAAAGTAAAATGCTGgtgagtttatttctgtattttgatgctcaaatgatgctttcaatgttgactagctgttagatgtgacattgaagatccaaatcctatcaataaccatttc

- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataacca