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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattcttttgcttttgcatgccttttcattcacatgttctctagttcttgaaattcattatttcttgttaatgctttcag

Basic information

species Vitis vinifera
transcript Vv04s0023g03620.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G08290.1 (Glycine max), 5'ss of exon 4
GTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattcttttgcttttgcatgccttttcattcacatgttctctagttcttgaaattcattatttcttgttaatgcttt-cag
||||||||||| |||| || || || || ||||| |||||||||||||||||||| ||||| |||||||| || || ||||| |||||||||||||||||||| |  |   | |  |||||       ||  | |   ||  | | ||||| ||     | | |  |  |  || ||| ||| |||
GTGAGATGAACCTAGCTGCTGGCATTCAGGTGGCACAATTGGCTCTTAAGCATCGGCAAAATAAAAAGCAACAGCAGAGGATTATTGTCTTTGCTGGAAGgtatgcttagctata-ttttgtgctatattgaaattgtattatttgtagttattttgtcttaattatcttgattcatgtttttcag

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G23590.1 (Glycine max), 5'ss of exon 4
GTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaatt-cttttgcttttgcatgccttttcattcacatgttctctagttcttgaaattcatt--atttcttgttaa--tgctttcag
||||||||||| |||| || || || || || || |||||||||||||||||||| || ||||| |||||||| |||||||| ||||||||||||||| |||  ||||  || || ||| ||  |   ||   |||    ||| || | ||   |  | | |||   |||   |||| |  | |||| ||
GTGAGATGAACCTAGCTGCTGGCATTCAGGTTGCGCAATTGGCTCTTAAGCATCGGCAGAACAAGAAGCAGCAGCAAAGGATTATTGTCTTTGCTGGAGGgtgtgaataactgtttcttctgtgttatttgatattgttttgt-ctgttgtgactatattccatctaattatctgtttaattccttttag

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G05250.2 (Glycine max), 5'ss of exon 4
GTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaatt-cttttgcttttgcatgccttttcattcacatgttctctagttct----tgaaattcattatttcttgttaatgctttcag
||||||||||  |||| || || || || || || |||||||||||||||||||| || ||||| |||||||| |||||||| ||||||||||||||| |||  ||||  || || ||| ||  |   ||   |||    ||| |   ||  ||    ||    | ||||| || | | | | |||| ||
GTGAGATGAATCTAGCTGCTGGCATTCAGGTTGCACAATTGGCTCTTAAGCATCGGCAGAACAAGAAGCAGCAGCAAAGGATTATTGTCTTTGCTGGAGGgtgtgaataactgtttcttctgtgttatttgaaattgttttgtccgtcaggactatattgcctctaattatctcgtttaattccttttag

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA01G36990.1 (Glycine max), 5'ss of exon 4
GTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattcttttgcttttgcatgccttttcattcacatgttctctagttcttgaaattcattatttcttgttaatgcttt-cag
||||||||||| |||| || || || || || || ||| |||||||||||||||| ||||| ||||| || || || ||||| |||||||||||||||||||| |  |   | |  |||||      ||   ||| | ||  | | ||||| ||     | | |  |     |||||| ||| |||
GTGAGATGAACCTAGCTGCTGGCATTCAGGTTGCACAACTGGCTCTTAAGCATCGGCAAAATAAAAAACAACAGCAGAGGATTATTGTCTTTGCTGGAAGgtatgcttagctata-ttttgtccatattgaaatt-atattatttgtagttattttgtcttaattatctaaattaatgtttttcag

upper sequence: Vv04s0023g03620.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G38630.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtag-gaattcttttgcttttgcatgccttttcattcacatgttctctagttcttgaaattcattatttcttgttaatgctttcag
| ||||| |||||| |||||| ||||||  | || ||  | |||||||||||||| |||||||| || || |  |||||||| ||||| ||||||||||||||  |||||  |||| ||||||        |  |  | | ||| | ||     |||  ||  |  | |  |  || |  ||| ||
GAGAGATCAACTTAACCGCAGCTATCCAGATCGCCCAGCTAGCTCTTAAGCATCGCCAAAACAAGAATCAACGCCAAAGGATTATTGTTTTTGCTGGAAGgtaccgaattgctttgtttttgctgagtaacttttgtata-gttttata----ctgatgtttttcttctgcttctact--ttttag

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|110724206|gb|EE099841.1|EE099841
EST:     CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|110718273|gb|EE094914.1|EE094914
EST:     CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|71865268|gb|DT014323.1|DT014323
EST:     CATCGGCAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|37185661|gb|CF605014.1|CF605014
EST:     CATCGGCAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|110723511|gb|EE100909.1|EE100909
EST:     CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|37188389|gb|CF607738.1|CF607738
EST:     CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|110702751|gb|EE079006.1|EE079006
EST:     CATCGGCAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|110384926|gb|EC949397.1|EC949397
EST:     CAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|110687737|gb|EE065489.1|EE065489
EST:     CATCGGCAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|110689406|gb|EE065602.1|EE065602
EST:     CATCGGCAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|110730475|gb|EE107599.1|EE107599
EST:     CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
EST: gi|71864038|gb|DT013093.1|DT013093
EST:     CATCGGCAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAG                         TCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA
genomic: CATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattc ... atgctttcagTCCTGTAAAGTATGACAAGAAGGTATTAGAGATGATTGGAAGAAAGCTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAGATGAACTTAGCCGCAGGTATCCAAGTGGCTCAATTGGCTCTTAAGCATCGACAAAACAAAAAGCAGCAACAAAGGATCATTGTCTTTGCTGGAAGgtaggaattcttttgcttttgcatgccttttcattcacatgttctctagttcttgaaattcattatttcttgttaatgctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG