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

GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttttaatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttctttatcagttcatatacctgt...

Basic information

species Vitis vinifera
transcript Vv11s0206g00130.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g73300.1 (Oryza sativa), 5'ss of exon 4
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttttaatttacaattgcattattttatgtatatagatc-cagtatatataaatagattgtcttt--ctctttccttctttatcagttcatatacctgt-
|||||||| |||||||| |||||| ||||||||||||| || |||||||||||||| ||||||||||| |||   | | ||    | ||| | || || |||   |||  || | ||||    ||   || |  |  |   |||||| |||    || |||  |    | 
GATCCTGCAGAGGCTGACAAGTTGCTGAAAATTCAGAGGGATTTGGATGAAACTAAGATTATTCTTgtaagta--actctatcgct-catgaattaatatatcctgattgcaatttataccc-tatgctggcaatggcatattccttatttcagtgtgcatggattcatg

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g64650.2 (Oryza sativa), 5'ss of exon 4
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttttaatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttctttatcagttcatatacctgt--
|| ||||| |||||||| |||||  ||||||| ||||| || ||||||||||| |||||||| || || ||| ||  ||  ||     |  | ||   | |||    | |  |  ||||   || ||   |   | |||    |  | |  |  |||   ||| |   
GACCCTGCAGAGGCTGACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtatttcttaccagaaaaaaaaattatagaatagctctgccattcatattggtaaata--ccaacacttcttgttctaacaaactcaatgacccgatc

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G178244_T01 (Zea mays), 5'ss of exon 4
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgag---------ttttaatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttctttatcagttcatatacctgt
|| |||||||| ||||| ||  |  ||||||||||||| || ||||||||||| |||||||||||||| ||         ||| ||| |   ||||| |||  |||  ||| |   |   | | | ||| ||    ||  ||      |  |   |||    |  ||        
GACCCTGCGGAAGCTGACAAACTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATTCTTgtaagcgtgatgtatttaaatcttttattgc-ttacattacatattttagttttgcaga-atatatgttatgcattgagtacttttgtattactgttcaatg-------

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 5
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta-atttacaattgcattattttatgtatatagatccagtatatataa-atagattgtctttctctttccttctttatcagttcatatacctgt--
||||||||||| ||||| || ||  ||||||||||||| || ||||||||||| |||||||| || || ||| | |  | |  || |   |||||   |  ||||   | |||| || | || ||  ||  |   | |   | ||  |  || | |    ||  || |  
GATCCTGCGGAAGCTGACAAATTAATGAAAATTCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtgtgatgtatttaaatcttttattgcttacatat---ttcagtttacagaatatgtatcatgcat-taagtactgttggattaatgttcattgctataa

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G19950.1 (Glycine max), 5'ss of exon 4
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttt----taatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttctttatcagttcatatacctgt
|||||||| |||||||| |||||| |||||||||||||||||||||||||||| ||||| || ||||| ||  |    || |||| | |||||  |   ||| |   |    ||   || | | |     |    || ||  |         ||    |||| ||  |  
GATCCTGCAGAGGCTGACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgcaatactttatatttgcaaaacagtatatgggtt--cccttcatcttttaccttctaaagttacttctcttcaagacattctgtcatgtagtt--

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA09G13840.1 (Glycine max), 5'ss of exon 4
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttt----taatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttctttatcagttcatatacc-tgt--
|||||||| ||||| || |||||| ||||||| |||||||||||||||||||| ||||| || ||||| ||       || || | | |||||  |      |||||| | | |  |  || |   |   |  |||     |     ||||||  |  |  | | || |||  
GATCCTGCAGAGGCAGACAAGTTGATGAAAATCCAGAGAGAGTTGGATGAAACCAAAATCATCCTTgtaagaacacaatacttcatatttgcaaaaca----gtatatgggttcccttcatct---tttgtcttctaaagttacttctctttaagacattctgtgccatgtag

upper sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 5'ss of exon 5
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttttaatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttc------tttatcagtt-catatacctgt----
|| || || |||||||||||| |||||||||| ||||| ||||||||||| || || ||||| ||||| |||  |   |        |  |  ||| |   | |||| ||  |||| ||||   |    || || |||    |||       ||  || ||  | |||  ||     
GACCCAGCAGAGGCTGATAAGCTGTTGAAAATCCAGAGGGAGTTGGATGAGACAAAGATTATCCTTgtaagtgctgtctc-------cggtcctttct---tgtagaccct-tatacataagcggtacttccttttctaagtttcagtatacttgccaattatacataaatgctgtt

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|351017097|gb|FQ424524.1|FQ424524
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|33408128|gb|CF213755.1|CF213755
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|349824324|gb|FQ417683.1|FQ417683
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|71881424|gb|DT030479.1|DT030479
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|33408558|gb|CF214185.1|CF214185
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|110390655|gb|EC955577.1|EC955577
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|71876275|gb|DT025330.1|DT025330
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|71866199|gb|DT015254.1|DT015254
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|110709953|gb|EE085862.1|EE085862
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|351028488|gb|FQ444769.1|FQ444769
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|110691734|gb|EE070172.1|EE070172
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|71876274|gb|DT025329.1|DT025329
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|110725014|gb|EE101356.1|EE101356
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|30125802|gb|CB911141.1|CB911141
EST:     AGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: AGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|294966596|gb|GW837731.1|GW837731
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAACTTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAAAAGCTGGACGGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|110709110|gb|EE084283.1|EE084283
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAAGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|71869605|gb|DT018660.1|DT018660
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|351018531|gb|FQ424638.1|FQ424638
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|351028310|gb|FQ427206.1|FQ427206
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
EST: gi|110371348|gb|EC935304.1|EC935304
EST:     ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTT                         CATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA
genomic: ATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagtttta ... tttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCCTGCGGAGGCTGATAAGTTGTTGAAAATTCAGAGAGAGTTGGATGAAACTAAAATTATTCTTgtgagttttaatttacaattgcattattttatgtatatagatccagtatatataaatagattgtctttctctttccttctttatcagttcatatacctgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctttcc