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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcttttgctttggacttggttcttcatatgtaaaggttatgcttgggttggtgtttgatacatgattatttctgtctgttttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTCACCCATTTTGAGGAG

Basic information

species Vitis vinifera
transcript Vv11s0016g03320.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 20
gtctgcttttgctttggacttggttcttcatatgtaaaggttatgcttgggttggtgtt-tgatacatgattatttctgtc-tgtt-ttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTCACCCATTTTGAGGAG
||| | |||| || |  | ||  || || |||    ||   |     |       |||| || ||  | | |     |  | |||| ||  |  |||||||||||||| ||||||||||  || ||| |||| ||||||||||||||||||||||||||||||||||| || ||||||||||||
gtcaggtttt-ctgtaaaatttattgttaatactcgaaaaattccagttttccactgttatgctagctaactccccttaccctgttattgctccagATTTGTGGAGACTGATGGTAAAGCTTTCGATAGAGTGAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTTACGCATTTTGAGGAG

upper sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 20
gtctgcttttgctttggacttggttcttcatatgtaaaggttatgcttgggttggtgtttgatacatgattatttctgtctgttttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTCACCCATTTTGAGGAG
||| |||||| || |  | ||| || || || | | ||    || |  |  ||    | | || | |   ||  |||   |   || ||  ||||||||||||||||||||||| |  |||||  |||| |||| ||| ||||||||||||||| |||||||||| || |||||||| |||
gtcagctttt-ctgtaaaattgattgttaatgtttgaaaa--attccagttttcaactgttatgc-tagctaactctccttaccttgttccagATTTGTGGAGACAGATGGTAAGGCTTTTGACAGAGTGAGGCAGACAGAAATTGGGAAGAAACATTTCAAACTTACGCATTTTGAAGAG

upper sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 20
gtctgcttttgctttggacttggttcttcatatgtaaaggttatgcttgggttggtgtttgatacatgattatttctgtctgttttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTCACCCATTTTGAGGAG
                    || | |||  |  ||||  || |  || |   |  ||||| | | | | | | || |     ||||  |  || ||||| ||||| ||||||||||| | |||||| || |||||||| || |||||||||||  |||| || || || ||||| || |||
-----------------gtatgatactttct-cgtaactgtaac-ctcgaactc-tgttt-aca-aggctgagttttaatattttttctccagGTTTGTAGAGACGGATGGTAAAGGTTATGATCGGGTGAGGCGGACAGAGATTGGGAAGAAGCATTTTAAGCTTACACATTTCGAAGAG

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|34550093|gb|CF518311.1|CF518311
EST:     GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAG                         ATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
genomic: GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAGgtctgctttt ... tttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
EST: gi|349828994|gb|FQ419526.1|FQ419526
EST:     GCCACTCCTACCATGCTAAATTGCCCCATGTACAAACTGTCATATTTCAG                         ATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
genomic: GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAGgtctgctttt ... tttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
EST: gi|351015564|gb|FQ426806.1|FQ426806
EST:     GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAG                         ATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
genomic: GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAGgtctgctttt ... tttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
EST: gi|34550961|gb|CF519167.1|CF519167
EST:     GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAG                         ATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
genomic: GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAGgtctgctttt ... tttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
EST: gi|351019618|gb|FQ439435.1|FQ439435
EST:     GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAG                         ATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
genomic: GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAGgtctgctttt ... tttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
EST: gi|349828615|gb|FQ418350.1|FQ418350
EST:     GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAG                         AGTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
genomic: GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAGgtctgctttt ... tttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT
EST: gi|351012697|gb|FQ430260.1|FQ430260
EST:     GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAG                         ATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTATGGCGGACTGAAAT
genomic: GCCACTCCTACCATGCTAAATTGCCTCATGTACAAACTGTCATATTTCAGgtctgctttt ... tttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttatgcttgggttggtgtttgatacatgattatttctgtctgttttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTCACCCATTTTGAGGAG
                  gtttgat  putative branch site (score: 5)
                               ttatttctgtctgttt  putative PPT
                       atacatgattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcttttgctttggacttggttcttcatatgtaaaggttatgcttgggttggtgtttgatacatgattatttctgtctgttttcttttagATTTGTGGAGACAGATGGTAAAGGCTTTGATCGAGTAAGGCGGACTGAAATTGGGAAGAAATATTTCAAACTCACCCATTTTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG