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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT

Basic information

species Vitis vinifera
transcript Vv04s0023g03110.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g03540.1 (Oryza sativa), 3'ss of exon 1
----ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
      |||    |   || |  ||    | |  |||| || | |   ||  || |  || |   |  | |  | |  |   || | ||     | ||| |  ||    ||  |||||||||| || ||||| |  |||||||| ||||||||| ||||||| | ||| || || |||||||||||||| || || ||||| ||
gtacaactagagatcgtatga-ttaat--ttgagtttcagagatgatcatt-gtggcattatttatcctaattgtgt-tgcctggtttgttgattgatgaa--gAACATTGTGGGATCGGGTACGATGAGCAAAGCGAGTGGTACTTCTTCAGCTACAAGGACAGGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACAAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g38834.1 (Oryza sativa), 3'ss of exon 2
----ggctaacact--ttcataagctagccatcgcatttctg-ataagtaaatccgttgtgttttccttgttcaaagcgaa--taattg-atctgaattataatggacagAGAGA----TGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
       |||   |  | ||||        ||  |||   || |||  || |||  | | | |  |  | |  | | |||   | ||      || |||    |||      |||    ||| |||| ||||| || |||||||  |||||||| ||||||||| ||||||| | ||| || || |||||||||||||| || || ||||| ||
gtttaattaatcttcatacatatatacttaatttcatgcatgcatagctagatcaatcgagctagctatatatagatcgatgctgatcatgcatggattggggtgggtgagaagAGCATTGCAGGATAGGGTACGAGGAGCAGAGCGAGTGGTACTTCTTCAGCTACAAGGACAGGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
--------ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
          |||||| | | || |  ||        | |  |   || || ||| |   |  |||   |  |         |   |||| ||||| |||   | ||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| || || |||||||| |||||
catatttgatctaacattataatta-ttatttgatctaatgttagcaa-tagatctgagttagtttttattctt----ttttttgctgatgtgaatgatat--ggcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
-------ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
         || |||  || ||   |     ||   || |  |     || ||| |||  |||||  |||||||       |   |||| ||||| |||   | ||||||||||| |||| |||||||| |||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| || || |||||||| |||||
atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgtta-gtttt--ttgttcatttttttt--ctgatgtgaatgatat--ggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattg-atctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
  |  |   ||  | ||    |   | |||   ||   |  | | |   | || ||    |  ||        ||  |||    ||| ||    | | |||||| |||| |||| ||||| || ||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||| || ||||| ||||| |||||
atcatattgttaaagaaatatggtctagcaaagctag-atcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
-ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttg---ttcaaagcgaataattg-atctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
  | |||     | ||   | ||| |      |  | || |||  ||   || | |||   ||    ||  |   | ||  |||    ||| ||    |   |||||| || | |||| ||||| || |||||||| |||||||||||||| |||||||| || |||||||||||||| ||||| || ||||| ||||| |||||
ttgttaaagaaat-atggtcaagcta----gatcttaattagtttatggtttttatttcttttaaatttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatgg--acagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
                 | ||   | || |   |   | ||  | |    | || ||    | ||        || ||     | |||| |||  |  |||||   ||| || ||||| ||||| || || ||||| |||||||| || || |||||||| |||||||||||||||||||| || || ||||||||||||||
-----------------gttacttaccgaacacc--gtgagatattttactttggttaaggtttt----attgattatcaccttaaattttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G36160.1 (Arabidopsis thaliana), 3'ss of exon 2
ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgtt---caaagcgaata-attgatctga-----atta-taatgg-----acagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
         ||||| ||  ||      ||||   | ||     | |   || | | ||| |  |    ||| | ||||| || |||||||     |||| | |||      | |||||| ||||| ||||| ||||| ||    ||||| |||||||||||||||||||| ||||||||||||||||| || || || || || |||||||||||
-------gttttcacaaaatacatgatgcatacttaatttaggatttttttct-tcttcttaatctgacaatgtgaatacatagatctgatgagcattaattatgtatattatagAGAGCTGCCGAATCGGATATGAGGAAAGAAATGAATGGTATTTCTTCAGCCACAAAGATAAGAAATATCCAACAGGAACAAGAACAAACAGAGCGACCAT

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
-ggctaacactttcataagctagccat----------cgcatttctgataagtaaatccgttgtgttttccttgttcaa-agcgaataattgat----ctgaattataatgga-----cagAGAGATGCCGGATCGGGTATG---------AAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT-
     ||||   ||||  |   | |||          || ||||||   |  || |    |||| ||    ||| |  | | |     | ||||     | |||| |  |||      ||| |  |||| |||||||| | |         |||| |||| ||| ||||| |||||||||||||||||||||||||||||    ||||   |  | ||| |||| |||   
gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatactgatgatattcaatttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------ggctaacactttcataagctagccatcgcatttctgataagtaaatccgt-tgtgttttccttgttcaaagcgaataattgatctgaa-ttataatgga--cagAGAGATGCCGGATCGGGTATGAAG---------AGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
                                                                         |    |    |  ||||  |||  || |   |    |||  || ||   | || |  | |  |    |  |  || |    ||||| | ||     |    |||||   ||| | || ||  | || |         | ||||  || ||||| ||||||||||||||||| ||||||||||| || || |   |  | ||  |         
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaa-tagatatggatatatatatatatatatatatatgagaatactctaagtactgataacacc--atctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------ggctaacactttcataag--ctagccatcgcatttctgataa-gtaaatccgt---tgtgttttcct----tgttcaaagcg---aata----------attgatctgaa----ttataatggacagAGAGATGCCGGATCGGGTATGA------AGAGCA---GAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
                                                                      |||| ||  |  ||  ||| |||| | |||      ||  |||   |       |||| ||||    | || | |||    |||           |||||    ||    ||  |  |  ||||    ||| |||||||| | ||      ||||||    | ||| ||||| ||||||||||||||||||||||| ||||| || || |   |  ||||  |         
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
-------------------ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgt---tttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
                    |||     ||||  ||   |   | ||   ||  ||  |||   | |||| |     | || |   |||  || |   ||  ||     ||   |   |||||  | ||||| || || |  |  |||||| | |||||||| |||||||||||||| || |||||||| || || |||||||||||||| ||||| |||  
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttgga--agtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
-------------------ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgt---tttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
                    |||     ||||   |   |   | | | ||  |   ||||   | |||| |     | || |   |||  || |   ||  ||     ||   |   |||||  | ||||| || || |  |  |||||| | |||||||| |||||||||||||| || |||||||| || || |||||||||||||| ||||| |||  
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaac-cgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT
                              aattgat  putative branch site (score: 4)
                           aataattgatctgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatggacagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- ctaacac
- - - - - - - - - - agccatc
- - - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - - - - aagtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagcga