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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT

Basic information

species Vitis vinifera
transcript Vv06s0004g01160.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 2
---gcatggatgcattttttaatttgacgaacgca-attgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT
     || |||| |  | |||  || |       | |  ||    ||||||       ||    |    | |    ||||||||     ||||    ||  ||||||||||| ||||| ||||||||||||||||| || ||||||||||| || || ||||| || || ||||| ||||| ||||| || |||||||| ||||
gacatatcgatgtacatattatgtttatttttttatagagtatatattatgttattgatatgctttactactttactcaatattaatgttgct----attatagGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACTTTTGGAATCAAGGGGGGTGCTGCTGGAGGTGGCTACAGCCAAGTCATACCCATGGATGAGT

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 2
-gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactg---ttaattaatgtcaatattctgt-ctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT
   |||  || ||    ||| ||  |  ||    ||||    ||  ||| |||  | |  | |   ||  || ||||    ||  |||  || || | |||| |||||||||| ||||| ||||||||||||||||| || || |||||||| || ||||||||||| || ||||| ||||| ||||| || |||||||| ||||
catatgtgtg-ataaaataactt--cagactgtcttgtaagtatc-tgctccagatcatgcggaagttgtttcatgtattaatgatgtattgttttttatgt-agGTTGTCACTTGCCTCCGTCAACCATCACAAGGGCCTACCTTTGGAATCAAGGGAGGTGCAGCTGGAGGTGGGTACAGCCAAGTTATACCCATGGATGAGT

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G13840.1 (Glycine max), 3'ss of exon 3
------gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT
         ||| | ||   | | |||  |  |   ||||  |      |||| |  |  ||     | ||  ||||  ||   |  | |||  || ||   |||||| ||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||| |||||||| || || ||||| ||||||||||| || |
ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgtatgtcaaagttatgctggatacataatccca---tcttatctctttttg---ttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G38740.1 (Glycine max), 3'ss of exon 2
------gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT
         ||| | ||   | | |||  |  |   ||||  |       ||| |  |  ||     | ||  ||||  ||   |  | |||  || ||   |||||| ||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||| |||||||| || || ||||| ||||||||||| || |
ctggttatttgggttcaagatattattgaaaaactacaatctttaatcgcatgtcaaagttatgctggatacataatccca---tcttatctctttttg---ttagGTAGTCACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGTGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G44010.1 (Glycine max), 3'ss of exon 2
--gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgt-caatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT
  |  |   ||  ||    |  || | | |   || | |     | |  | |     |||  | |   |  ||    |||    | |   ||  |  |||||||| || |||||||||||||||||||| |||||||| |||||||||||||||||||| ||||| |||||||| || || ||||| ||||||||||| || |
caggttatttgggttcaagatattaatggaa--aactataactttcaatcgcttgtcaaagttat-gctggatacataatcccatcttatctctttttgttagGTAGTTACCTGCCTTCGTCAACCATCGCAAGGACCTACTTTTGGAATTAAAGGAGGCGCAGCTGGTGGTGGCTATAGCCAAGTTATTCCCATGGATGAAT

upper sequence: Vv06s0004g01160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G50480.1 (Arabidopsis thaliana), 3'ss of exon 2
gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT
   |     | |  ||| |||| |  | |  |    |  || ||           |||  | |   ||  | |  || |      || |  || |  |||||||| || || ||||| ||||| ||||||||||| || |||||||| |||||||||||||| |||||||| || ||||| |||||||| ||||| ||||
--gttctctcttgctttcattt-attagcttatgccttatgcttgc-ttttggacaaacttctctctttgtattgatttgtgaagtgttgttgct--tagGTTGTTACTTGTCTTCGCCAACCGTCACAAGGACCCACCTTTGGAATCAAAGGAGGTGCAGCTGGTGGTGGGTATAGTCAGGTGATTCCTATGGATGAGT

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|352764253|gb|FQ471233.1|FQ471233
EST:     CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAG                         GTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
genomic: CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAGgtaatacttt ... atgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
EST: gi|352773998|gb|FQ473130.1|FQ473130
EST:     CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAG                         GTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
genomic: CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAGgtaatacttt ... atgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
EST: gi|352774080|gb|FQ474603.1|FQ474603
EST:     CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAG                         GTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
genomic: CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAGgtaatacttt ... atgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
EST: gi|352776569|gb|FQ474871.1|FQ474871
EST:     CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAG                         GTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
genomic: CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAGgtaatacttt ... atgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
EST: gi|352776755|gb|FQ472642.1|FQ472642
EST:     CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAG                         GTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
genomic: CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAGgtaatacttt ... atgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
EST: gi|352768983|gb|FQ468174.1|FQ468174
EST:     CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAG                         GTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
genomic: CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAGgtaatacttt ... atgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
EST: gi|352764844|gb|FQ471904.1|FQ471904
EST:     CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAG                         GTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA
genomic: CTACCACTGTTGGTCTCTGTCAAGCTTTGGGAGCTTTTCTTGATAAAAAGgtaatacttt ... atgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT
                   aattaat  putative branch site (score: 3)
                 ttaattaatgtcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatggatgcattttttaatttgacgaacgcaattgtggtgattatgccccaagtaaaactgttaattaatgtcaatattctgtctgcttatgatgttagGTTGTCACCTGCCTTCGTCAACCATCACAAGGACCAACTTTTGGAATTAAAGGAGGTGCAGCAGGTGGTGGTTACAGTCAAGTGATTCCCATGGACGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - ggatgca
- - - - - - - - - - - - -gaacgca
- - - - - - - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - gccccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaac