Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactatggtgcagtgacacatatgcagctttaatctttgcacgtcaactttttgcttaggcttttattgttgatgatgtgtcatctgcctttgtgtatctgttctttataattgtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATTGCTTGTGTTGGGGAGACTCTTGAGCAGCGAGAATCGGGATCTACAATGG

Basic information

species Vitis vinifera
transcript Vv06s0004g04800.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G146206_T01 (Zea mays), 3'ss of exon 1
gtaaactatggtgcagtgacacatatgcagctttaatctttgcacgtcaactttttgcttaggcttttattgttgatgatgtgtcatctgcctttgtgtat--ctgttctttataattgtgaatg-cagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATTGCTTGTGTTGGGGAGACTCTTGAGCAGCGAGAATCGGGATCTACAATGG
                       ||||  | | |  |||||    |||||    |  || |  || |   || |  || |  ||| ||||  ||| |  ||  || ||||||||     |  ||| ||||||||||  ||||||||||||||||||||  | |||||  | || || ||||||||  |||| ||||| ||||||||| ||||  | ||| | |||||||
-----------------------tatgt-gttgtgttcttt---tgtcaagccat--ctaaacctgtacctgcttctgttaagtcttctgtattttttaattacttttctttatttcaattcatggcagTTTGTTGCTGATAAAGTTGCATATGCACTCACTCAAGGTCTCAAGGTAATTGCTTGCATTGGTGAGACCCTTGAGCAGAGAGAGGCAGGAACAACAATGG

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 4
gtaaactatggtgcagtgacacatatgcagctttaatctttgcacg--tcaactttttgcttaggcttttattgttgatgatgtgtcatctgcctttgtgtatctgttctttataattgtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATTGCTTGTGTTGGGGAGACTCTTGAGCAGCGAGAATCGGGATCTACAATGG
||| |   || |  | || |     |  |  ||   |  ||  |    || ||||| ||     |||| || ||   |  |  |  ||| | |       ||  | || |     | |||  || |||||||| |||||||||||||| |||||||||   |||||  ||||||| || || ||  ||||||| |||||||| ||||| ||| | ||  | |||| ||
gtacaaagtgttcaattggccttgctttatattctcttgttaaaaaattctactttgtgaagttgcttgtaatggcaaaaacataacatttac-------taaatatttt-----actgtctat-cagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTGAAAGTTATAGCATGCATTGGGGAAACTCTTGAACAGCGTGAAGCTGGTACAACAACGG

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 4
gtaaactatggtgcagtgacacatatgcagctttaatctttgcacgtcaactttttgct-taggcttttattgttgatgatgtgtcatctgcctttg--tgtatctgttctttataattgtgaatgc-agTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATTGCTTGTGTTGGGGAGACTCTTGAGCAGCGAGAATCGGGATCTACAATGG
               ||   |  | | ||  |     | ||||     |   ||||| | ||   | |  ||  ||| | ||  |    || |        ||||  ||  | |   || |   | | ||||||| |||||||||||||| |||||||||   |||||  | ||||| ||||| ||  ||||||||||||| || ||||| ||| | ||  | |||| ||
---------------gtacaaagtgttcaatt---gcccttgctttatattcttttgttataaattctactttgtgaagttgcttataatggcaaaaatcatatcatttactaaatgttttacttcctagTTTGTGGGAGATAAAGTTGCCTATGCACTTCAACAAGGTCTAAAAGTTATTGCATGCATTGGGGAGACTCTCGAACAGCGTGAAGCTGGTACAACAACGG

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|110415564|gb|EC981483.1|EC981483
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|351028511|gb|FQ444792.1|FQ444792
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|30129525|gb|CB914864.1|CB914864
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110389346|gb|EC954175.1|EC954175
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|22015534|gb|BQ800568.1|BQ800568
EST:     TTTAGCTG-ATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|33409412|gb|CF215039.1|CF215039
EST:     TTATTCTTGGTCATTCTGAAAG-AGATCTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|294965195|gb|GW837026.1|GW837026
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110378426|gb|EC943557.1|EC943557
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110692722|gb|EE068329.1|EE068329
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110395870|gb|EC961544.1|EC961544
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|349826936|gb|FQ419027.1|FQ419027
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|161710111|gb|FC059796.1|FC059796
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110726667|gb|EE102647.1|EE102647
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|71871008|gb|DT020063.1|DT020063
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|294963951|gb|GW836826.1|GW836826
EST:     TTATTGTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110404715|gb|EC970203.1|EC970203
EST:     TTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|161720486|gb|FC070598.1|FC070598
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|161714171|gb|FC062916.1|FC062916
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110364963|gb|EC928597.1|EC928597
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|110411583|gb|EC977303.1|EC977303
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
EST: gi|33409496|gb|CF215123.1|CF215123
EST:     TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG                         TTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT
genomic: TTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAGgtaaactatg ... gtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgatgatgtgtcatctgcctttgtgtatctgttctttataattgtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATTGCTTGTGTTGGGGAGACTCTTGAGCAGCGAGAATCGGGATCTACAATGG
 tgttgat  putative branch site (score: 4)
                                    tttataattgtgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactatggtgcagtgacacatatgcagctttaatctttgcacgtcaactttttgcttaggcttttattgttgatgatgtgtcatctgcctttgtgtatctgttctttataattgtgaatgcagTTTGTTGGAGATAAAGTTGCATATGCACTTTCCCAAGGCTTGAAAGTGATTGCTTGTGTTGGGGAGACTCTTGAGCAGCGAGAATCGGGATCTACAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG