Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccaaaagtgaagttataaattgtttttggatggtatatgaatgaatatttgacatgtttgttatagtcatttataattatttttcactttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATTAGACAAGAATATGAGCGGAAGGCAAAGCAGGTGGAAATTCGAAGGAAAA

Basic information

species Vitis vinifera
transcript Vv08s0056g00620.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00620.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S269_15V6.1 (Physcomitrella patens), 3'ss of exon 1
gtccaaaagtgaagttataaattgtttttggatggtatatgaatgaatatttgacatgtttgttatagtcatttataattatttttcactttgtttc----tagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATTAGACAAGAATATGAGCGGAAGGCAAAGCAGGTGGAAATTCGAAGGAAAA
 || |    |||     |   |     |    |   || | |   | | |   ||| || | |||||      |  |||  | ||      || |||     ||||||||||||||||||| || ||  | || ||||||||||||||||| ||| | || || | |||||| ||||  ||||| |||||| ||||  | ||||
-tcaattgatgattccgttggtaaggctc---ttccatgttatcaactgtgcaacacgtgtcttatatcggaattaaatgttgttgaggggtggttcaacgcagGAATTCAACATTGAGAAGTTACAGATTGTAGAAGCTGAAAAGAAGAAAATTCGGCAGGAGTTTGAGCGTAAGGAGAAGCAAGTGGAAGTTCGCCGTAAAA
















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|349832600|gb|FQ421958.1|FQ421958
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110698903|gb|EE076929.1|EE076929
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110723106|gb|EE100040.1|EE100040
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|351023437|gb|FQ432820.1|FQ432820
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|294963783|gb|GW836633.1|GW836633
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|351013904|gb|FQ434056.1|FQ434056
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110376043|gb|EC941082.1|EC941082
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110411460|gb|EC977174.1|EC977174
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110702891|gb|EE079258.1|EE079258
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|351017341|gb|FQ435693.1|FQ435693
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|294966352|gb|GW837603.1|GW837603
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|349819240|gb|FQ412134.1|FQ412134
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110702889|gb|EE079256.1|EE079256
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|161718482|gb|FC066332.1|FC066332
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110687935|gb|EE065911.1|EE065911
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|77587268|gb|DV222769.1|DV222769
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110702890|gb|EE079257.1|EE079257
EST:     TGCAGGAGGCGGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|110362618|gb|EC926164.1|EC926164
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|71859327|gb|DT008382.1|DT008382
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
EST: gi|351015182|gb|FQ445466.1|FQ445466
EST:     TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAG                         GAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT
genomic: TGCAGGAGGCCGAAGAGAAAGCTAACGAAATCTCTGTTTCTGCTGAAGAGgtttttattt ... ttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatttgacatgtttgttatagtcatttataattatttttcactttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATTAGACAAGAATATGAGCGGAAGGCAAAGCAGGTGGAAATTCGAAGGAAAA
   atttgac  putative branch site (score: 4)
                                    tttttcactttgtttc  putative PPT
             tttgttatagtcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccaaaagtgaagttataaattgtttttggatggtatatgaatgaatatttgacatgtttgttatagtcatttataattatttttcactttgtttctagGAATTCAACATTGAGAAATTGCAACTAGTTGAAGCTGAAAAGAAGAAGATTAGACAAGAATATGAGCGGAAGGCAAAGCAGGTGGAAATTCGAAGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- ccaaaag
- - - - - - - - - - - - - - tggatgg
- - - - - - - - - - - - - - - - - - - - -aatgaata
- - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtt