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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgtttctgcctgcaattgtacgagtattactttgttagcaatcattgtacttcagctcttttctcagcaattaagtaatttgacctctgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACTGTGCTGGAGAAGATTGAGGCCGTTGTTCAAAGCAAGCCAAAGCGACCTG

Basic information

species Vitis vinifera
transcript Vv05s0051g00650.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G19000.1 (Glycine max), 3'ss of exon 3
---acatgtttctgcctgcaattgtacgagtattactttgttagcaatcattgtacttcagctcttttctcagca-attaagtaatttgacctctgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACTGTGCTGGAGAAGATTGAGGCCGTTGTTCAAAGCAAGCCAAAGCGACCTG
     | ||   ||  ||| ||| |     |   |  |   | ||||  || | ||||  ||  || |   |  |  |||  |  | ||   | |      |||||||||||||| ||||| || || |||||||| ||  | ||||| |||  |||| ||||||||||||| || ||||||||||||||||||||||| ||||
cacgaaagtaattga-tgccattcttaatttgagatataacttgcaagaat-gaactt--gccattgtaatattatgttattttttctgttttgttttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTACTGACTCCTGTTGTGATGGAGAAGATTGAAGCTGTTGTTCAAAGCAAGCCAAAGCGCCCTG

upper sequence: Vv05s0051g00650.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G24620.1 (Glycine max), 3'ss of exon 3
------acatgtttctgcctgcaattgtacgagtattactttgttagcaatcattgtacttcagctcttttctcagcaattaagtaatttgacctctgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACTGTGCTGGAGAAGATTGAGGCCGTTGTTCAAAGCAAGCCAAAGCGACCTG
      | |  ||  ||||     |  |  ||    ||  |||  || ||| ||| | |    |   | || ||     |||  |  | ||   ||||     |||||||||||||| ||||| || || |||||||| ||  |  |||| |||  |||| |||||||||||||||| |||||||||||||||||||| || ||||
cataaaagaaattgatgccattcttaatttgatatataacttgcgag-aatgattttgccatcgtaatattatc-----ttattttttctgttttctgttgctcagATTCAAGAGAACATGAAAGCAATCGATGTCATTCCATTATTGACTCCTGTTGTGATGGAGAAGATTGAGGCTGTTGTTCAAAGCAAGCCAAAACGCCCTG
















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|110714394|gb|EE091251.1|EE091251
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|22012551|gb|BQ797585.1|BQ797585
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|110700435|gb|EE078471.1|EE078471
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAA                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGAC
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGAC
EST: gi|110705491|gb|EE082401.1|EE082401
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|110427791|gb|EC994242.1|EC994242
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|110715171|gb|EE092916.1|EE092916
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAAGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|110386404|gb|EC950997.1|EC950997
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|30330182|gb|CD013444.1|CD013444
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|110409766|gb|EC975436.1|EC975436
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|110705588|gb|EE082610.1|EE082610
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT
EST: gi|110362011|gb|EC925517.1|EC925517
EST:     CAAATCCGAATGTCTCATCAGTTATTACTGGGGCAACAAAGGAGTCTCAG                         ATTCAAGAGAATATGAAGGCTATTGAAGTCATACCTCTGCTGACACCTACT
genomic: CAAATCCGAATGTCTCATCAGTTATTACTGGGGCGACAAAGGAGTCTCAGgtcagtttta ... tgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtacttcagctcttttctcagcaattaagtaatttgacctctgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACTGTGCTGGAGAAGATTGAGGCCGTTGTTCAAAGCAAGCCAAAGCGACCTG
                                   atttgac  putative branch site (score: 4)
                                         cctct  CT-rich tract
                          aattaagtaatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgtttctgcctgcaattgtacgagtattactttgttagcaatcattgtacttcagctcttttctcagcaattaagtaatttgacctctgggatgcagATTCAAGAGAATATGAAGGCTATTGATGTCATACCTCTGCTGACACCTACTGTGCTGGAGAAGATTGAGGCCGTTGTTCAAAGCAAGCCAAAGCGACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
acatgtt
- - - - - -cctgcaa
- - - - - - - - - - - - - - - - - - - - gcaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacctc