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'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC

Basic information

species Vitis vinifera
transcript Vv08s0007g06190.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g41110.1 (Oryza sativa), 3'ss of exon 1
ctaacaattctgat-ttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
||  |  | ||  |  |  |    |         |   || |||| |||  |      | |    | |  |||  |||   | | ||   | ||  |||||||||| ||||| ||||| ||  ||||||||||||||||||| |||||||| |||||||||||||| ||| | ||||||||  |||  ||||| ||    |
cttgctttactcctgctagtgcagagaccaacagtttctatatttgttacttgtaagggcctttttaatattaatctt-cattgtttatgttaatatgcagCTTGTACGCAGTAACAGTCGCCGGTTTATGCCTTCACAAGCAGATGAAGAAGCTCATCAATTATCTTATCTGCAAAAGCATATGGTCAACATTCTGAGTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G026962_T02 (Zea mays), 3'ss of exon 1
------ctaacaattctgatttcttatttatgtagttg-atacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
      | | | |||||| || |   | |    ||||| | ||  | |  |||||| |  | ||     ||| |   ||  | |||   | ||   |||  |||||| |||| || ||||| || ||  | ||||||||||||||||| |||||||| ||||||||  |||| ||||||||||||||  || | ||||| ||  |||
gttgcaccatctattctg-ttgccagtatggagagttggagacacataacttttatttcttatttgtcgactta---tagacatat---gcttatgtcattttgcagTTTGTACGGAGCAATAGTCGCCGTTTTATGCCTTCACAAGCAGATGAAGAAGCTCATCAGCTATCGTATTTACAAAAGCATATGACCAACATTCTAACAC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G180690_T01 (Zea mays), 3'ss of exon 3
ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC-----------
    ||  |   |||||  ||   |  | | | ||    ||||||  |  |  | |     |  ||   |||   |||| ||  ||        ||||||||||| ||||||||||||||  | ||||||||||| ||||| ||||||||   |||||| || |||| | | ||||||||  |||| || || ||| | |           
----catcttccatttcaaatggttagattggctat---aattttcaaaatcatctc--tgacatgcctttaa--ttatttcaatttatattttttgcagcttgttcgcagCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTCTCTTGGCAGAT

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G145376_T01 (Zea mays), 3'ss of exon 1
---ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
    || |  | |||   ||||   | |  | | | ||  |    | || |   |   |     |  ||   |||   |||| ||  ||        ||||||||||| ||||||||||||||  | ||||||||||| ||||| ||||||||   |||||| || |||| | | ||||||||  |||| || || ||| | |
gttttagctgtgctgccatcttccatttcaaatggttagattggctattcaaaat-catctctgacatgcctttaa--ttatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G417658_T02 (Zea mays), 3'ss of exon 1
ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttaccctta-----tctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
 || |    |||   |||| | | |  |||      ||| ||| | |||    |    ||| |    |  | || |||     ||     |  ||    ||||||||||| ||||| ||||||||  | ||||||||||| ||||| ||||||||   |||||| || |||||| | ||||||||  |||| || || ||| | |
-tagctgcgctgccatcttctatttcaagtga----ttagattgtctataacttaaaatcacatctgatctgcctttaattattccaaactatatggttttgcagCTTGTTCGCAGTAACAGCCGTCGTTTTATGCCTTCTCAAGCTGATGAAGAAATTCATCAGTTGTCCTATCTGCAAAAGCATATGGCGAATATTCTTACTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G072227_T01 (Zea mays), 3'ss of exon 1
ctaacaattctg--atttcttattt-atgtagttga--tacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
  | |  | |||  || |   |||| |  | |||    |   || | |||| |   |   |     |  ||   |||   |||| ||  ||        ||||||||||| ||||||||||||||  | ||||||||||| |||||  |||||||   |||||| || |||| | | ||||||||  |||| || || ||| | |
--agctgtgctgccatcttccatttcaaatggttagattggctataattttcaaaat-catctctgacatgcctttaa--ttatttcaatttatattttttgcagCTTGTTCGCAGCAACAGCCGCCGTTTTATGCCTTCTCAAGCTAATGAAGAAATTCATCAGTTGTCCTTTCTGCAAAAGCATATGGCGAATATTCTTACTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G29860.1 (Glycine max), 3'ss of exon 1
ctaacaattctgatttcttatttat--gtagttgatacttaa--attttttatg-ttgtgttgtcaaa--ctgaacttacccttatctcggt-tcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
          | |||| |||||     ||  | | | |||    |||  ||||| || | ||        ||   ||     | ||   | | |  |     |||||||| || ||||||||||| ||| |||||||||| || || || ||||||||||| |||||||| || ||| | ||||||||||||||||||||  | || |
--------atttatttattattagctggtgatcggtgctttttcattcgttatgattctatttctgtttcctattctgttgttgattctgatgttaaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCACATCAATTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G32750.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------ctaacaat-tctgatttcttatttatgtagttgatacttaaattttttatg-ttgtgttgtcaa------actgaactta----cccttatctcggt-tcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
                                                   |||    | | ||||||||   |||    | ||  | ||   ||||   || || ||||||  |      ||| ||||      |  | ||   | | | ||     |||||||| || ||||||||||| ||| |||||||||| || || || ||||||||||| ||||| || || ||| | ||||||||||||||||||||  | || |
gtattctttattttttagctggtgtttggtgcttttttgttcgtgatgactctatttctatttgatttctgtattaaactgctggcaattttgttttgagtgattctgttgttgatttgatactaaactagaaagcgttgattctgatattgaatgttttgcagCTCGTACGCAGCAACAGTCGGCGGTTTATGCCGTCCCAGGCTGATGAAGAGGCGCATCAGTTGTCGTATCTGCAAAAGCACTTGGCTAACATTGTGTCTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G42230.1 (Arabidopsis thaliana), 3'ss of exon 1
---ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
    || | ||  |  || || |||  |||   |   |  |   |           ||| |      |||  |||   | |  |   ||  ||||  ||||||||||| || |||||||||||  |||||||||| ||||   | |||||||| |||||||||||||| ||| | ||||||||| | || || ||  |||| |
attttaccgataattgtt-ctcattactgtttctatcatatgggtagagacatccttgtagctg--ttgagtttaagttaaatttcctttcatcatcttgcagCTTGTTCGTAGCAACAGCCGTCGGTTTATGCCATCACCGACAGATGAAGAAGCTCATCAATTATCGTATCTGCAAAAGCACATTGCAAATATTATTTCTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G57890.1 (Arabidopsis thaliana), 3'ss of exon 1
ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaac---ttacccttatctcggttcgatcaaat-tgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
   ||  ||||    | || | |   |  |    || |   |         | | |||   | || ||    |||    ||||||  ||  ||||  | |||||||||| ||||||||||||||  | |||||||| ||||| || ||||| || |||||||| || || ||| | ||||| || || || |||||| |||| |
--cactgttctttggtattctatcgtttctcatcacatgggtcgaaccaactttattg--gagctaaaattgttatttatatctccttttcatcatttctgcagCTTGTTCGCAGCAACAGCCGTCGATTTATGCCATCACAGGCAGATGATGAAGCTCATCAGTTGTCATATCTGCAAAAACATTTAGCAAACATCATTTCTC

upper sequence: Vv08s0007g06190.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G57890.2 (Arabidopsis thaliana), 3'ss of exon 2
ctaacaattctg--atttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaat-tgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
      |||||    ||||| ||  |  | | |   ||  |  || ||   | |        ||| ||   |||    ||||||  ||  ||||  | |||||||||| ||||||||||||||  | |||||||| ||||| || ||||| || |||||||| || || ||| | ||||| || || || |||||| |||| |
----gtattctatcgtttctcatc-acatgggtcgaaccaactttattggagcta-------aaattg---ttatttatatctccttttcatcatttctgcagCTTGTTCGCAGCAACAGCCGTCGATTTATGCCATCACAGGCAGATGATGAAGCTCATCAGTTGTCATATCTGCAAAAACATTTAGCAAACATCATTTCTC

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|37185143|gb|CF604496.1|CF604496
EST:     CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAG                         CTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
genomic: CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAGgtgatttttt ... caaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
EST: gi|110359462|gb|EC920979.1|EC920979
EST:     CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAG                         CTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
genomic: CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAGgtgatttttt ... caaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
EST: gi|161717410|gb|FC065289.1|FC065289
EST:     CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAG                         CTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
genomic: CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAGgtgatttttt ... caaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
EST: gi|110725032|gb|EE101381.1|EE101381
EST:     CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAG                         CTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
genomic: CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAGgtgatttttt ... caaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
EST: gi|110690216|gb|EE067119.1|EE067119
EST:     CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAG                         CTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG
genomic: CGTCGACGTCGGCTTTTGATGGGTATTTGTCAGCGTTGTCGCCACTCCAGgtgatttttt ... caaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC
                     aacttac  putative branch site (score: 2)
                                           atcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaacaattctgatttcttatttatgtagttgatacttaaattttttatgttgtgttgtcaaactgaacttacccttatctcggttcgatcaaattgcagCTTGTCCGCAGCAACAGCCGGAGGTTTATGCCTTCACAAGCCGATGAAGAGGCTCATCAATTATCCTATTTACAAAAGCACTTGGCTAACATCCTTTCAC

ctaacaa
- - - - - - - - - - - - - - - - - - - - - - - - tgttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaact