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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGCAACCACAAAAAGTTCCCTCTGGGCACTATGCAGCAGTGACTGATATTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgttgcttgaggtacaaaaagtattttgtgaactagtcttactcgcctgtgcaatgacactgttatatgctttcagtgctgatttttgttatag...

Basic information

species Vitis vinifera
transcript Vv01s0011g04130.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G41620.1 (Glycine max), 5'ss of exon 6
TTGGCAACCACAAAAAGTTCCCTCTGGGCACTATGCAGCAGTGACTGATATTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgttg-------cttgaggtacaaaaagtattttgtgaactagtcttactcgcctgtgcaatgacactgttatatgctttcagtgctgatttttgttatag-
|||||  |||||||| ||||||||||| || | |||| |||||||||||||||||||||| || |||||||| ||| |  | || ||||||  |||||||||| ||| ||         |      ||||||  |||  |||  |    || |       | |   ||    || ||||  | ||||| |    | ||   ||  |  
TTGGCTGCCACAAAAGGTTCCCTCTGGTCATTTTGCATCAGTGACTGATATTGCATGGGCTAGATCTGGTGATTATATTATGTCCGTCAGTCATGACCAGgtatttttttaaaacacattctgtccacaaaagctatactgttgatccatcatgtctat-tattttat----ctattat--gatttca-tatgaacttgaatttcaaa

upper sequence: Vv01s0011g04130.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA20G25600.1 (Glycine max), 5'ss of exon 6
TTGGCAACCACAAAAAGTTCCCTCTGGGCACTATGCAGCAGTGACTGATATTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgttgcttgaggtacaa--aaagtattttgtgaactagtc-ttactcgcctgtgcaatgacactgttatatgctttcagtgctgatttttgttatag
|||||  |||||||| || |||||||| || | |||| |||||||||||||||||||||| || |||||||| ||| |  | || ||||||  |||||||||| ||  ||     |  | |     |   |   | |  |||| |  | | ||   | |   ||   |    | |||| ||||| |   || ||   ||  | 
TTGGCTGCCACAAAAGGTCCCCTCTGGTCATTTTGCATCAGTGACTGATATTGCATGGGCTAGATCTGGTGATTATATCATGTCCGTCAGTCATGACCAGgtatttatttaaaacacattctgttcacaaaggctatatactattgatcaatcatgtctattattttatctat-tatgatttca-tatggacttgaatttca-
















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|351031220|gb|FQ445047.1|FQ445047
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|349832389|gb|FQ420950.1|FQ420950
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|34547373|gb|CF515605.1|CF515605
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|351054132|gb|FQ450214.1|FQ450214
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|351038018|gb|FQ460760.1|FQ460760
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|351016289|gb|FQ446149.1|FQ446149
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|351036140|gb|FQ463985.1|FQ463985
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|352793961|gb|FQ479203.1|FQ479203
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|110371641|gb|EC935756.1|EC935756
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|351054298|gb|FQ450381.1|FQ450381
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|351043253|gb|FQ443974.1|FQ443974
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
EST: gi|349817591|gb|FQ407381.1|FQ407381
EST:     TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAG                         ACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC
genomic: TTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgtt ... aactttgcagACAACTCGAATTTTTGCATCTTGGCAAAATGAAGCTAGTTTTGGAGGTAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGCAACCACAAAAAGTTCCCTCTGGGCACTATGCAGCAGTGACTGATATTGCATGGGCCAGGTCTGGTGAATATTTGCTCTCAGTCAGTGCTGACCAGgtaatttgttgcttgaggtacaaaaagtattttgtgaactagtcttactcgcctgtgcaatgacactgttatatgctttcagtgctgatttttgttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaaaa