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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttggttgaaatctgtttgtaggacaaacaagattttatttactgtgatttcttttctgatcgacctctttgcttgcttcag

Basic information

species Vitis vinifera
transcript Vv14s0068g01280.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G05470.1 (Glycine max), 5'ss of exon 5
GTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttggttgaaatctgtttgtaggacaaacaagatttt---atttactgtgatttcttttctgatcgacctctttgcttgcttcag
|||||  || |||||||||| ||| | ||||||||||| |||||||| || |||||||||| |||||||| |      || ||    ||||  || |||    |   ||||   || || | || | | |||  |    || ||  |||  |  |||||
GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACTGGAAGgtgt------gtgga----tgttgttatgactggtatagttttcaaatatagtatgttctatttctttgctgatctacttgactatttcag

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G07260.1 (Glycine max), 5'ss of exon 5
GTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttggttgaaatctgtttgtaggacaaacaagatttt---atttactgtg-atttcttttctgatc-----gacctctttgcttgcttcag
|||||  || |||||||||| ||| | ||||||||||| ||||| || || |||||||||| |||||||| |         |||   | ||| | | |||| || || |||   || || |  | |||||||  ||||       ||||| ||||| || || ||
GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCCATCAACCGAAAGCAAACTGGAAGgtgt---------gaatgttatttattgaacaatcatgactttttaatataataagtatttcttagctgactttaatgacctatttgcctgttttag

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA19G27360.1 (Glycine max), 5'ss of exon 5
GTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttggttgaaatctgtttgtaggacaaacaagatttt---atttactgtgatttcttttctgatcgacctctttgcttgcttcag
|||||  || |||||||||| ||| | ||||||||||| |||||||| || ||||||||||  ||||||| |      || ||    ||||  || |||        ||||   || || | |  | | |||  |    |||||  |||  |  |||||
GTTCGTGTTTCTGAGTATAACAATATCCGCAGTCAGCTTAATGCTATCAACCGAAAGCAAACAGGAAGgttt------gtgga----tgttgttatgactggtctagttttctaatatagtatattctttttctttgctgacctacttgactatttcag

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA16G26220.1 (Glycine max), 5'ss of exon 5
GTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttggttgaaatctgtttgtaggacaaacaagatttt--atttactgtg-atttcttttctgatc-----gacctctttgcttgcttcag-
|||||  || | |||||||| ||| | ||||||||||| ||||| || || |||||||||| |||||||| |         |||   | ||| | |  ||| || || |||  || || |    |||||||  ||||       ||||| ||||| || ||    
GTTCGTGTTTCCGAGTATAACAATATCCGCAGTCAGCTTAATGCCATCAACCGAAAGCAAACTGGAAGgtgt---------gaatgttatttattgaccaatcatgacttttaatataatacatatttcttagctgacttaaatgacctatttgcctgtttttag

upper sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G12840.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttggtt---gaaatctgt-ttgtagga-caaacaagattttat--------ttactgtgatttcttttctgatcgacctctttgcttgcttcag
|||||  ||||||| ||||| ||| | ||  |||| |||||||| ||||| ||||||||||||||||||||   |||   |    | || | |  | || || || || |||   | |        |  |    |    ||||    |     |  |    |   | | 
GTTCGTGTTGCTGAATATAACAATATCCGTGGTCAACTCAATGCCATTAACCGAAAGCAAAGTGGAAGgtaattcttttcttctcatatttatactataagagcacactagaaactgtgggcggtttagcaacaacaaattttgaagtttgttttctcatctatctga-

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|351031454|gb|FQ446657.1|FQ446657
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|349830231|gb|FQ420491.1|FQ420491
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|351024893|gb|FQ433310.1|FQ433310
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|71881861|gb|DT030916.1|DT030916
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|110699022|gb|EE077184.1|EE077184
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|110693329|gb|EE069475.1|EE069475
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|349833078|gb|FQ416456.1|FQ416456
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|71882447|gb|DT031502.1|DT031502
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|27581998|gb|CB004693.1|CB004693
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|161716182|gb|FC069494.1|FC069494
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTTCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|351013608|gb|FQ429749.1|FQ429749
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|71883798|gb|DT032853.1|DT032853
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|351020303|gb|FQ445910.1|FQ445910
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|71887796|gb|DT036851.1|DT036851
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|110693330|gb|EE069469.1|EE069469
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|110700866|gb|EE077894.1|EE077894
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
EST: gi|349830278|gb|FQ420538.1|FQ420538
EST:     AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAG                         CCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC
genomic: AATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttg ... cttgcttcagCCTAGCTGTTCGTGATCTTTCCAACCTAGTAAAGCCAGAGGACATTATTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGCATTGCTGAGTATAATAATGTGCGCAGTCAGCTCAATGCTATTAATCGAAAGCAAAGTGGAAGgtataccttggttgaaatctgtttgtaggacaaacaagattttatttactgtgatttcttttctgatcgacctctttgcttgcttcag

- - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG