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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttctttctctctctctctctctctctctgaataaatatatttgtggatttgttgtttgtttgtttgtttggctaaccctaggtgcggattcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGGAGTTCGAATTGTGTCTAAGAGCGAAGCTGAAGTG

Basic information

species Vitis vinifera
transcript Vv11s0016g01770.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G16650.3 (Glycine max), 3'ss of exon 1
------gtaatcttctttctctctctctctctctctctctg-aataaatatatttgtggatttgttgtt-tgtttgtttgtttggctaaccctaggtgcggattcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGGAGTTCGAATTGTGTCTAAGAGCGAAGCTGAAGTG
       |   | ||| |||| |||||||||||||||| ||  ||   | |   ||||  |   |  || ||||||  | ||  || ||    |  |   | |  |||  || ||| | ||||||||||||| |||||| |||||||| |||||||||||||||||||||||||| ||| |||  || |  ||||  
gtgagtctcgccctctctctccctctctctctctctctttgtgatgtgtgtgaatgtgattgattaattatgtttggcttttgagccaattg-aattattggtatgtg-tagGACTGAAAGTGGGACTTTTAAGGATGGGGATCTGCTTGTCAACAGGGATGGAGTTCGAATTGTCTCTCAGAATGATGTCGAAGCT

upper sequence: Vv11s0016g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G06020.1 (Glycine max), 3'ss of exon 1
gtaatcttctttctctctctctctctctctctctgaataaatatatttgtggatttgttgtttgtttgtttgtttggctaaccctaggtgcggattcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGGAGTTCGAATTGTGTCTAAGAGCGAAGCTGAAGTG
       |   ||||||||| ||| | |   | ||  | ||| |  |||   |||  || |  |||||  | |||| | ||    |  ||  | |   |   || ||| | ||||||||||||| |||||| |||||||| |||||||||||||||||||||||||| ||| |||  || |  ||||  
------gtgagtctctctctttctttgtga-tgtgtgtgaatgtgattg---attaattat--gtttggct-tttgaccaaattgaattgttggtattt---agGACTGAAAGTGGGACTTTTAAGGATGGGGATCTGCTTGTCAACAGGGATGGAGTTCGAATTGTCTCTCAGAATGATGTCGAAGCT

upper sequence: Vv11s0016g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G16650.2 (Glycine max), 3'ss of exon 1
------------gtaatcttctttctctctctctctctctctctctg-aataaatatatttgtggatttgttgtt-tgtttgtttgtttggctaaccctaggtgcggattcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGGAGTTCGAATTGTGTCTAAGAGCGAAGCTGAAGTG
             |   | ||| |||| |||||||||||||||| ||  ||   | |   ||||  |   |  || ||||||  | ||  || ||    |  |   | |  |||  || ||| | ||||||||||||| |||||| |||||||| |||||||||||||||||||||||||| ||| |||  || |  ||||  
gttcctgtgagtctcgccctctctctccctctctctctctctctttgtgatgtgtgtgaatgtgattgattaattatgtttggcttttgagccaattg-aattattggtatgtg-tagGACTGAAAGTGGGACTTTTAAGGATGGGGATCTGCTTGTCAACAGGGATGGAGTTCGAATTGTCTCTCAGAATGATGTCGAAGCT

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|110719234|gb|EE096979.1|EE096979
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|110711245|gb|EE087537.1|EE087537
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|33404398|gb|CF210025.1|CF210025
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|294966771|gb|GW837790.1|GW837790
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|71862252|gb|DT011307.1|DT011307
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|110403013|gb|EC964035.1|EC964035
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|110699630|gb|EE076797.1|EE076797
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|71862576|gb|DT011631.1|DT011631
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|33404467|gb|CF210094.1|CF210094
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|110712219|gb|EE089588.1|EE089588
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|161718247|gb|FC065681.1|FC065681
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|30252938|gb|CB970489.1|CB970489
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|161717958|gb|FC069259.1|FC069259
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|161721441|gb|FC070444.1|FC070444
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
EST: gi|110699026|gb|EE077196.1|EE077196
EST:     AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCT                         AACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG
genomic: AATCTCAAGCTCACTCTCCCTCCTGATGAGGATTCATTGACTAAGTTCCTgtaatcttct ... ttcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatttgttgtttgtttgtttgtttggctaaccctaggtgcggattcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGGAGTTCGAATTGTGTCTAAGAGCGAAGCTGAAGTG
                          ggctaac  putative branch site (score: 2)
           tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttctttctctctctctctctctctctctgaataaatatatttgtggatttgttgtttgtttgtttgtttggctaaccctaggtgcggattcgtggcagAACTCAGAGTGGGACTTTTATGGATGGTGATCTGCTGGTCAACAGGGATGGAGTTCGAATTGTGTCTAAGAGCGAAGCTGAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG