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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgtttatgctttgccttcctttgggtgggtatacttactttatccatctcctgactcacttggcag

Basic information

species Vitis vinifera
transcript Vv09s0018g01710.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 4
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgtttatgctttgccttcctttgggtgggtatacttactttatccatctcctgactcacttggcag
| ||||||||||| ||  | || || ||| | || ||||| || ||||||||||||||||||  ||| ||  |||||||||||||||||  |    | ||   | ||||        ||||||   || ||  | |||||   |  || ||  | |||| ||||||                  
GAAAGTATGTTGGGAACCGCCCTATTAAATTGCGTAAGAGTAACTGGAAGGAGAGGACAGATGTTGAGGCTCTGGAAAGACAAAAGgtacttgtctatttccttctttaa-------atgttttctctctgtgt-cctttaatttcgtcta--tgcttt-tccatcgttcag------------

upper sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA11G01300.1 (Glycine max), 5'ss of exon 5
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgtttatgctttgcc-ttcctttgggtgggtatacttactttatccatctcctgactcacttggcag
| ||||||||||||||| |||| || |||||||| ||||| || ||||||||||||||||||| ||||||  |||||| ||| |||||     | ||  |||             |  |||  ||| ||||   ||  |||   ||  | | || |||| || | |||  ||  | |  || |||
GAAAGTATGTTGGAAATCGGCCGATAAAACTACGCAAGAGTAAGTGGAAGGAGAGGACAGATTATGAAGCACTGGAAAAACAGAAGgt-----cgcaacttt-------------ctttgtaaatgatttgaaattgtttttaatgtatgt-ctaacttaattcttctattg-tttaaatgacag

upper sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G36570.1 (Glycine max), 5'ss of exon 5
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttcca-tgtttatgctttgccttcctttgggtgggtatacttactttatccatctcctgactcacttggcag
| ||||||||||||||| | || || |||||||| ||||| || |||| |||||||||||||| ||||||  |||| | ||| ||||||    ||   || | |||  | |  ||  | |  || || |   | |  | ||  ||  ||  |   |||| || | |||  ||  | || ||||||
GTAAGTATGTTGGAAATCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtag---caattttctttgtcaatgatttgaaattgttctgttaaacttagccttttgtatgtcca---acttaattcttctattg-tttacatggcag

upper sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G30900.2 (Glycine max), 5'ss of exon 5
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgttta-tgctttgccttcctttgggtgggtatacttactttatccatctcctgactcacttggcag
| ||||||||||||||  | || || |||||||| ||||| || |||| |||||||||||||| ||||||  |||| | ||| ||||||    ||   || | |||  | |  ||  |  | |  || |     |  | ||  ||  |   ||  |||| || | |||  ||  | || ||||||
GTAAGTATGTTGGAAACCGTCCTATAAAACTACGCAAGAGTAAGTGGAGGGAGAGGACAGATTATGAAGCACTGGAGAAACAGAAGgtag---caattttctttgtcaatgatttgaaattatgctgttaaatgtaaccttttgtatg---accaacttaattcttctattg-tttacatggcag

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|349828848|gb|FQ419181.1|FQ419181
EST:     AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG                         AACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
EST: gi|110728709|gb|EE104516.1|EE104516
EST:     AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG                         AACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
EST: gi|27583752|gb|CB006447.1|CB006447
EST:     AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAA-G                         AACCATATCCAAAAGAAACCAAAGCTTTCAAAG
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAAAGAAACCAAAGCTTTCAAAG
EST: gi|351028807|gb|FQ433237.1|FQ433237
EST:     AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG                         AACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
EST: gi|33404798|gb|CF210425.1|CF210425
EST:     AGGGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG                         AACCATATCCAAA
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAA
EST: gi|351016422|gb|FQ423849.1|FQ423849
EST:     AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG                         AACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
EST: gi|349819739|gb|FQ402676.1|FQ402676
EST:     AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG                         AACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
EST: gi|110416231|gb|EC982198.1|EC982198
EST:     AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAG                         AACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG
genomic: AGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcac ... cacttggcagAACCATATCCAAAAGAAACCAAAGCTTTCAAAGAAGAGCATATTGCATAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGTATGTTGGAAATAGGCCAATCAAACTACGGAAGAGCAATTGGAAGGAGAGGACAGATTCTGAAGCCTTGGAAAGACAAAAGgtatattcacacttttgtgtttacggcttccatgtttatgctttgccttcctttgggtgggtatacttactttatccatctcctgactcacttggcag

- - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC