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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctgttttgttttattttattcttttattttttatttctctatttaattctaaggcttcctgagcaattcaaattctaatatgtgaggatgtacatttggccag

Basic information

species Vitis vinifera
transcript Vv14s0060g01290.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 9
AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctgttttgttttattttattcttttattttttatttctctatttaattctaaggcttcctgagcaattcaaattctaatatgtgaggatgtacatttggccag
| ||||| |||||||| ||  | |||||||||||| | |||||||| |||||||||||| | ||||||||||  | |   || |   ||   | | |||  |||  || || |  || | |  ||  | |   | |   | || |  ||  |                          
ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaacttttcattttaacatcgcaatatttggtttgatacttttggatctgaa-ctctgacaagcaggctattttatcttacag-------------------------

upper sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA10G28890.2 (Glycine max), 5'ss of exon 9
AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctgttttgttttattttattcttttattttttatttctctatttaattctaaggcttcctgagcaattcaaattctaatatgtgaggatgtacatttggccag
| ||||| |||||||| ||  |||||||||||||| | |||||||| ||||| |||||| | ||||||||||       |||   || ||  ||   | || ||  || || | ||| |||  ||  | |   |     | || |  ||  |                          
ATTTCAAGGATGACCCCGACCTCTATGTTTTCCCCAACTTGAAGTACGTGGGGATTGAATTGTGGCAGgtaa-----acttttaatttttacatcgctatagttgatacttttgtatctaaa-ctctgacaagcaagctattttatcttacag-------------------------
















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|33401772|gb|CF207399.1|CF207399
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|110381806|gb|EC935430.1|EC935430
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|351056636|gb|FQ443263.1|FQ443263
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|349816036|gb|FQ413550.1|FQ413550
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|351027478|gb|FQ444727.1|FQ444727
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|349808465|gb|FQ405609.1|FQ405609
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|352794106|gb|FQ479348.1|FQ479348
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|349826885|gb|FQ418976.1|FQ418976
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|29781779|gb|CB346544.2|CB346544
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|110687446|gb|EE064865.1|EE064865
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|351043138|gb|FQ451311.1|FQ451311
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|351022735|gb|FQ428644.1|FQ428644
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|33402080|gb|CF207707.1|CF207707
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|77578221|gb|DV217893.1|DV217893
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|110708716|gb|EE086573.1|EE086573
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAA                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
EST: gi|349810157|gb|FQ401603.1|FQ401603
EST:     AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG                         GTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG
genomic: AGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctg ... atttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAGgtaatgtctgttttgttttattttattcttttattttttatttctctatttaattctaaggcttcctgagcaattcaaattctaatatgtgaggatgtacatttggccag

- - - - - - - - - - - - - - - - - - - TTGAAG