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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATCTTCGCTCGCTATTCAGAAGGAATTCAAAGACAGGGCTTCGCGGATTGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaattgaattggcttgtattttaatttgattgttctgacgttataatgattttaacaacatatagcatctgcgttaactgggatgtttttaggtc...

Basic information

species Vitis vinifera
transcript Vv11s0016g04370.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04370.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S142_96V6.1 (Physcomitrella patens), 5'ss of exon 1
--CGATCTTCGCTCGCTATTCAGAAGGAATTCAAAGACAGGGCTTCGCGGATTGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaattgaattggcttgtattttaatttgattgttct--gacgttataatgattttaacaacatatagcatctgcgttaactgggatgtttttaggtc
        | |||| ||   |||  ||| || ||  |  | || |||| ||| ||   | | |||||||||||||| ||||||||| |||| ||||| ||||||||||       | || |  | | |  |   ||||||| |  |  | ||  |||    |   ||      ||  ||    |||| ||  ||  |  |    
CCTACGACTGGCTCCCTG--CAGTCGGAGTTTAACAAGCGTGCGTCGCAGATCGGGCTTAGTATTCATCAGACCTCTCAGAAGCTCTCCAAACTAGCCAAATgtgagttgccttgtaggttaatttgtgcagaagattgttgttggggggtaggatgggactg-taatggtaggcgcctatcgtaac-ggtgtgcatggaatgt

upper sequence: Vv11s0016g04370.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S47_13V6.1 (Physcomitrella patens), 5'ss of exon 1
CGATCTTCGCTCGCTATTCAGAAGGAATTCAAAGACAGGGCTTCGCGGATTGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaattgaattggcttgtattttaat-ttgattgttctgacg----ttataatgattttaacaacatatagcatctgcgttaactgggatgtttttaggtc
| | |  ||   ||  | |||  ||| |||||  |  | || |||| ||| ||   | | |||||||||||||||||||||||| ||||| |||| ||||||||||   | | |||    | |  ||||| |||   |    || |    || |||    |     |   |     || |  |  || || |   ||| |     
CAAGCGACGGGTGCCTTACAGTCGGAGTTCAACAAACGAGCGTCGCAGATCGGGCTTAGCATTCATCAGACCTCGCAGAAGCTCTCCAAGTTAGCCAAATgtgagt---taatttgtaaggcagcttaatgttggacggcaggatggtgtttgtaagatctggtgtattttgagatatttatgggaattgtgtgctttctgaa--
















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|351030339|gb|FQ432277.1|FQ432277
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|71859003|gb|DT008058.1|DT008058
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|351020053|gb|FQ445660.1|FQ445660
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGAATCCA-CAATGGAGATCCAAGAA
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGA-TCCAACAATGGAGATCCAAGAA
EST: gi|349816228|gb|FQ403724.1|FQ403724
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349816405|gb|FQ403780.1|FQ403780
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCTAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAGCAATGGAGATCCAATAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349821277|gb|FQ404409.1|FQ404409
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349819358|gb|FQ412252.1|FQ412252
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349811748|gb|FQ409745.1|FQ409745
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349821040|gb|FQ404293.1|FQ404293
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349814061|gb|FQ414319.1|FQ414319
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349814073|gb|FQ414331.1|FQ414331
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349824758|gb|FQ414616.1|FQ414616
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGGTGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|351017491|gb|FQ435844.1|FQ435844
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
EST: gi|349814372|gb|FQ398812.1|FQ398812
EST:     TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAAT                         TGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT
genomic: TGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaatt ... gtatcaccagTGGCAAAGAGGACATCAGTTTTTGATGATCCAACAATGGAGATCCAAGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATCTTCGCTCGCTATTCAGAAGGAATTCAAAGACAGGGCTTCGCGGATTGGATATGGGATTCATCAGACCTCGCAGAAGCTCGCCAAGCTAGCGAAATgtgagtaattgaattggcttgtattttaatttgattgttctgacgttataatgattttaacaacatatagcatctgcgttaactgggatgtttttaggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaca