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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT

Basic information

species Vitis vinifera
transcript Vv13s0019g00910.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 4
ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT
  ||| |  ||    | ||    | | || || ||    |         |     |  |  ||||   ||||   || |  || || || |  | | ||||||||||| |||||  | || || || |||||||| || ||||| |||||||| ||||| |||||| |||||||||| 
tgttgatgtatgccctggtccattaacttctgtttgcatcagtagaaactaatcaatgtgcatgttgctttagttaatttgctgtgctttttttatgcagGTTGAAAGTATAGTTCTGAGCATCATTTCAATGCTCTCTAGTCCGAATGACGAGTCTCCAGCAAATATTGAAGCTGCC

upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 4
ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggtt-ctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT
   | |  |||    |  | || | |  |     |||      |   |   |    ||  |||  ||| || | ||  | | ||| |||    |||| |||||||||||||||||  | || || ||||||||||| || ||||| |||||||| ||| | |||||  |||| || |||
-gatacagaatgctttgttttggtcaggtacttctttcatgtgtgagtacttttgtatgctatcactagttgttaagttgattattgttatccatttgcagGTTGAAAGCATAGTTCTGAGCATTATATCAATGCTCTCTAGTCCAAATGACGAGTCTGCAGCAAACATTGAGGCAGCT

upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G04470.1 (Glycine max), 3'ss of exon 4
-ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaacta-actatg-gttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT
  |||   || ||   ||||   |  | |||||||||  | | ||   | |   |  |||| |   ||  |||||||   | | |||   | ||   || ||||| || || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| ||||||||||||||||| 
gtttttgccacttc--ttgtcc-accacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCG

upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 4
-ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaacta-actatg-gttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT----------------------
  |||   || ||   ||||   |  | |||||||||  | | ||   | |   |  |||| |   ||  |||||||   | | |||   | ||   || ||||| || || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| |||||||||||||||||                       
gtttttgccacttc--ttgtcc-accacttgtggtttgacatactagttgtaaagctatttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCAGCAAATGTTGAAGCTGCGGTAAGTTTGACCATTTTGTGAT

upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 4
ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaacta-actatg-gttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT
 |    |   |    ||||   |    || ||||||  | |  |   | |   |   ||| |   ||  |||||||   | | |||   | ||   || ||||| || || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| ||||||||||||||||| 
-tgatatgcgtcttcttgtcc-accgcttttggtttgacatagtagttgtaaagctgtttaaaacctgcttatgaattaatattatatatgctgtcttgcagGTAGAGAGTATAGTATTAAGTATCATATCGATGCTTTCTAGTCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCG

upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G14980.2 (Glycine max), 3'ss of exon 4
ctttgctca--attaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT----------------------
 ||||  ||  | ||     | |   || ||||  ||| |     |     | |  | |  | || | |||| ||  |   |    |  |  ||  || ||||| || || ||||| || ||||| ||||||||||| || || |||||||| |||||||| |||||||||||||||||                       
ttttgtccatcactagcaaatttatatacttgtcatttgtgaagttaaaagttt--ttacatcatatgtattaatatattaatacgttatgttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCAGTAAGTTTGATCATTTCTTATT

upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 4
ctttgctca--attaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT
 ||||  ||  | ||     | |   || ||||  ||| |     |     | |  | |  | || | |||| ||  |   |    |  |  ||  || ||||| || || ||||| || ||||| ||||||||||| || || |||||||| |||||||| ||||||||||||||||| 
ttttgtccatcactagcaaatttatatacttgtcatttgtgaagttaaaagttt--ttacatcatatgtattaatatattaatacgttatgttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCAATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCA

upper sequence: Vv13s0019g00910.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G06960.1 (Glycine max), 3'ss of exon 4
ctttgctcaattaagttgtgtg-attatttgtggtttt---tcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT
         |||   || |||  |  | | |    |||   | ||  || |||  |   | |||| |   |  | ||  |   || ||||    ||  || ||||| || || ||||| || ||||| ||||| ||||| || || |||||||| |||||||| ||||||||||||||||| 
-gaaatggtattgcattttgtccaccactagcaaatttatatacttttcacttgttataagttttctaagtcatgatatattaaaatatg---ttatcttgcagGTAGAGAGTATAGTATTGAGTATCATATCGATGCTTTCCAGCCCTAATGATGAATCTCCTGCAAATGTTGAAGCTGCA

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|110706214|gb|EE081542.1|EE081542
EST:     ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACG                         GTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC
genomic: ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACGgtattatcta ... taattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC
EST: gi|34318943|gb|CF371697.1|CF371697
EST:     ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACG                         GTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC
genomic: ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACGgtattatcta ... taattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC
EST: gi|110408251|gb|EC973881.1|EC973881
EST:     ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACG                         GTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC
genomic: ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACGgtattatcta ... taattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC
EST: gi|110687133|gb|EE064279.1|EE064279
EST:     ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACG                         GTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC
genomic: ACCCAAATGGCTACGAGCTGGCAACAGAACGCTGGTCCCCAGTCCATACGgtattatcta ... taattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT
                                                ttttc  CT-rich tract
         taattttatgtctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgctcaattaagttgtgtgattatttgtggtttttcctcctctctttctcgtaattttatgtctatttatgaaactaactatggttctaattttcagGTTGAAAGCATAGTCTTAAGTATAATATCAATGCTGTCAAGTCCTAATGACGAATCTCCCGCAAATGTTGAAGCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - tgtgtga
- - - - - - - - - - - - - -ttgtggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa