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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT

Basic information

species Vitis vinifera
transcript Vv04s0008g01170.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 4
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctca--tgtggttgttttc-catgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                                                        |  |    ||        |       | ||  |||       ||   |||  ||      |  | || ||| |     |||| | ||| |||||||||||||||||||| ||||| ||||||||||| ||||| ||||| | ||||||||||||||| ||||| || |||||||| || || |||||
------------------------------------------------------------------------gtttgaattctgaaagatctgaatggctaat-tccttgtttactgaacttattcctgtgtagttctgattgataaaatatgtgt-agGCCTTGGTCTAAATGAAGAGGTTCAACCAAGCATGGAATCTAATACGAAATTCAGTGATGTAAAGGGTGTCGATGAAGCCAAAGCTGAACTTGAGGAAAT

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 4
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaaca-tccccaccctctcttctttctctctctcatgtggttgttttccatg---ttt---cagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                                                           | |  |  ||        |  ||  |  | |   |     || | ||     ||| |  |||| || |  || |||   |||    ||| |||||||||| | |||| || ||||| | |||||| || || |||||||| | ||||||||||||||||||||| || |||||||| || || |||||
--------------------------------------------------------------------------gtttggttttctgaaatatctgaatgactaattttctagacctttactggacttctttgctgtgattctgatcgatgaaatttgtgtagGTCTTGGTCTAAGTCAAGAAGTTCAACCAATCATGGATTCTAAAACAAAATTCAGTGATGTAAAGGGTGTTGATGAAGCCAAAGCTGAACTTGAGGAAAT

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 4
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctct-ctcatgtggttgttttccat--gtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                                                                   |    |       ||  |        | | | |   |      ||  | |||       || |  ||    |  ||| |||||||| ||||||||||| ||||| ||||| || || | ||||||||| | ||||||||||||||||||||| |||||| |||| || ||||||||
----------------------------------------------------------------------------------gtttgatttttgtgaaagatatgtattatcttttgaacggcaagtcagcccattaaccctttatagattgaatgtagGTCTTGGTCTGAATGAAGAGGTTCAACCAAGCATAGAGTCTACTACAAAATTCAGTGATGTAAAGGGTGTTGATGAAGCAAAATCTGAACTTGAAGAAAT

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 3
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                                                                   |    |      | | |   ||    | | |||    |      |||        ||  |        |  ||| |||||||| ||||| ||||| ||||| ||||| || || || |||||||| | ||||||||||||||||||||| |||||| |||| || ||||||||
----------------------------------------------------------------------------------gttagatattgttagagagttatatt-atcttctgaattgaacagctcattaaccatttatgaattgaatgtagGCCTTGGTCTGAATGAGGAGGTTCAACCAAGCATTGAGTCTAAAACAAAATTCAGTGATGTAAAGGGTGTTGATGAAGCAAAATCTGAACTTGAAGAAAT

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 2
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                                       |  |     ||   ||  ||| |    || || |        |     |||   |         | |  ||| |    |||   | |||   || |  ||||||||||| |||||||||| |||||||||||||||||||||| ||||||||||| ||||||||| ||||||||||||||||| |  ||||| ||||||||
-----------------------------------------------------gtattccttgttagtgta-acctgtttgtattctttttttattga-----atctgaatttagcagacatgttctttggtttgt---tttttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTTGATGAGGCAAAGGAAGAGCTGGAAGAAAT

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 4
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                            ||| ||   | |        || |||     |||  | ||  | |       ||     ||          | ||||||   |        || || |||   || |  ||||||||||| |||||||||| |||||||||||||||||||||| ||||||||||| ||||||||| ||||| ||||||||||| |  ||||| ||||||||
-------------------------------------------gtattccttgttagtg-----taacctttttgtatttttattttattttattgaatctgaatttagcagacatgttctttggtt--------tgatt-tttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G10960.1 (Glycine max), 3'ss of exon 2
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                                       |  |     ||   ||  ||| |    || || |        |  |      |     |            ||| |  | || || |||   ||||  ||||||||||| |||||||||| || ||||||||||||||||||| ||||||||||| ||||||||| ||||| ||||||||||| |  ||||| ||||||||
-----------------------------------------------------gtattccttgttagtata-acctgtttgtattctttttttttttattattgaatctgaatttagcagacatgttctttggtttgttt-tttcatatgtcccagGACTTGGTATAAATGAAGAAGTTCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT

upper sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
                                                                        |  |       |  ||| |     | | || | |   |     |    ||   |||  | || |   || ||   |  | | |||||||||| |  | ||||| ||||||||||| ||||| || |  || ||||||  ||||||||||||||||||||| ||||| ||||||||||| |||||
-------------------------------------------------------------------gtagagtttggttgtgttttcttcagt-gatccaatagctgtattgaatgactttgtgctcattaattta--tgcttaatacatgttagGACTTGGTTTGCACGAAGAAGTGCAACCTAGTATGGATTCGAGCACCAAATTTTCTGATGTAAAGGGTGTTGATGAAGCAAAGGCTGAGCTAGAGGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT
         ccctctcttctttctc  CT-rich tract
                                     ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA