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

...agtttgctttatttgattctgatatatttttgtgaattggtaattgggctatatgcagtttaaattgttaaacgtgaaactgatgtctcattttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04800.t01
intron # 3
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 3
lower sequence: GLYMA15G04290.1 (Glycine max), 3'ss of exon 3
---agtttgc-tttatttgattctgatatatttttgtgaattggtaattgggctatatgcagtttaaattgttaaacgtgaaactgatgtctcattttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG
    || ||  ||  | |||||   | | | |   |   |          |  | ||  ||  ||   ||  ||   ||  |  |  | | |    ||  |||||||||| |||||||| |||||||| ||||||||||||||| ||||||| |||||| | ||    ||||||  |||||||||||||
ccccgtctgtgttggtgtgatttataaaaagtgaggcacacattctcaaagcttttacccatctt---ttaatagctgtacattttgtcttttgcatta-acagTGCTGAAATGCTTGTTAATTTGGGAATTCCTTGGGTTATTATTGGTCACTCTGAACGGAGGCAGCTTTTAAATGAATCAAATGAG

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 3
--agtttgctttatt--tgattctgatatatttttgtgaattggtaattgggctatatgcagtttaaattgttaaacgtgaaactgatgtctcattttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG
      ||  | ||   ||||    | ||| |   |   |||        |  | ||  ||  ||   ||  ||    |  |  |  | | |    ||  |||||||||| |||||||| |||||||| ||||||||||||||| ||||||| |||||| | ||    |||||   |||||||||||||
cgtccctgtgtcatcagtgatatataaatagtgaggcacattttctcaaagtttttacccatctt---ttaatagctttccattttgtcttttgcatta-acagTGCTGAAATGCTTGTTAATTTGGGAATTCCTTGGGTTATTATTGGTCACTCTGAACGGAGGCAGCTTTTGAATGAATCAAATGAG
















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:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACCGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|351028511|gb|FQ444792.1|FQ444792
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|30129525|gb|CB914864.1|CB914864
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACCGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|110389346|gb|EC954175.1|EC954175
EST:     AACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: AACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|294965195|gb|GW837026.1|GW837026
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACCGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|110378426|gb|EC943557.1|EC943557
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|110692722|gb|EE068329.1|EE068329
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|110395870|gb|EC961544.1|EC961544
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|349826936|gb|FQ419027.1|FQ419027
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|161710111|gb|FC059796.1|FC059796
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|110726667|gb|EE102647.1|EE102647
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACCGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|71871008|gb|DT020063.1|DT020063
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|294963951|gb|GW836826.1|GW836826
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTGTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|161720486|gb|FC070598.1|FC070598
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|161714171|gb|FC062916.1|FC062916
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|110364963|gb|EC928597.1|EC928597
EST:     GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: GCACAAAACTGTTGGATTCGGAGAGGAGGTGCTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
EST: gi|110411583|gb|EC977303.1|EC977303
EST:     CTTTCACCGGTGAGATCAG                         TGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC
genomic: CTTTCACTGGTGAGATCAGgtatgttttt ... ttttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggctatatgcagtttaaattgttaaacgtgaaactgatgtctcattttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG
                                aactgat  putative branch site (score: 3)
                                        tctcatttt  CT-rich tract
           agtttaaattgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttgctttatttgattctgatatatttttgtgaattggtaattgggctatatgcagtttaaattgttaaacgtgaaactgatgtctcattttgcacagTGCTGAGATGCTTGTCAATTTGGGCATTCCTTGGGTTATTCTTGGTCATTCTGAAAGAAGAAGTCTTTTAGCTGAATCAAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - -tatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctca