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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaactttagttggcgatcagctttgccttcttttattttttctttttttct...

Basic information

species Vitis vinifera
transcript Vv10s0116g00360.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 5
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaa--ctttagttggcgatcagctttgccttcttttattttttctttttttct--
|||||||||| || |     || |||||||||||||| ||  ||||||||||||| ||||| ||||||||||| || ||||||||||||||  |||| |||| |||  |     ||| |   | |     |  |   | |||| |||       |||||||||  | | |      ||||  | || | ||  |  | |     
AAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGTACTTCAGgt-tggccc---ctaatatgtgtaaccctgttcttttgcttcttaggcaattttctttagttgctgttgacaaagacctttgtgtactgttgatgctctgtcaa

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 5
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaactttagttggcgatcagctttgccttcttttattttttctttttttct--------------------------------------
|||||||||| || ||    ||||||||||||||||| ||  ||||||||||||| ||||| |||||||| ||||| ||||| |||| |||| |||||||||  | | |        | | ||||      |||  |    || |  | |||  | |  | ||| |     || | || || |  || |||                                               
AAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgctaacgctgtgttttgacctttcaatataagg-ctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 5
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaactttagttggcgatcagctttgccttcttttattttttctttttttct--------------------------------------------------------------------
|||| ||||||||||||  |||||| || |||||||| ||  |||| |||||||| |||||||||||||| ||||| |||||||||||||| || || |||| ||    || | |||||| ||  | |  ||||| | | ||| |||  |   || |  | |  ||||  ||| | |  |  | |||  | |   ||                                                                       
AAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGAATTTCAGgtttgtcttagctgaattttatttctggtgtaatcta-tgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 5
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaactttagttggcgatcagctttgccttcttttattttttctttttttct------------------------------------------------------------------------
|||| ||||||||||||  |||||| || |||||||| ||  |||| |||||||| |||||||||||||| ||||| ||||| |||||||| ||||| |||| ||    || | |||||| ||  | |  ||||| || |  ||   || | |||| |||   ||  |    ||  ||| | |   ||||   |||   |                                                                        
AAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGAACTTCAGgtttgtcttagctgaattttatttctggtgtaatctaggtcttattaggaagcttttgttaatga--aatgatgttttcatgttgctttttaatttacatacaaggacatttccatttatgaatatgtacagtgatcctgtttgtgcaatgctttaatatggattcatgcag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G39380.1 (Glycine max), 5'ss of exon 5
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaat------------tttgttgataggataatcaagtttctaagggggaactttagttggcgatcagctttgcc--ttcttttattttttctttttttct------------------------------
|||||||||||||||    ||||||  | ||||| |||||  |||| ||||||||||||||||||||||||||||| ||||| ||||||||  | || ||||    |  |||  ||             | |||| ||  | |    || ||  |  |     || | ||      || | ||||      | |     | || || ||| | |                              
AAGCTGAAGAAACAGTGCAGAAGCTAAACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCAAACACAAATGCATGCCTCCTTGCTGAGCATTTCAGgttctatgaagggaaaaattacctttccatctgttcatctgttgtataatttgtttggcatacacatgagagaaaaattacctttcataaatatgcagctgttcctgtttctttaactatttctgtttaatttggattatacag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 5
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca-ggtcaattttgttgataggataatcaagtttctaagggggaa----ctttagttggcgatcagctttgcct---tcttttattttttctttttttct------------------------------
||||||||||||||||   ||||||||||||||||||  |  | || || ||||||||||| || ||||| |||||||||||||||||||||||||| ||||          ||  | | ||||     || | | |  | ||| ||| | ||     | |  |||  ||||    |  ||    ||||| || ||| ||  ||                                  
AAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAAACTTCAGgtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggcgaaagtagttgttcttgaagatccatgtgaccagaatctttaatatttgctgattcagcatttgacttattatctacttgtataattag

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 5'ss of exon 5
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaactttagttggcgatcagctttgccttcttttattttttctttttttct-
|||||||||| || | |   ||| | ||||| ||||| ||  | || ||||||||||||||||| || || |||||||| || ||||||||| |||||||||     |    |  |  |||||  || ||| |   ||  ||         ||||   |  |   |  | |||    | |  | |  | |    |||||  
AAGCTGAAGAGACTGTTACAAAGATGGATTTAGATGGTCTTGTGGTAATTGGTGGAGATGACTCCAATACTAATGCTTGTCTCCTTGCTGAACACTTTAGgta----attttttgaaattgtt--taagattaatgagactc---------acttctctctgttttgtgttttaatgtttggtttcctattcggttttcag

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|351027672|gb|FQ446839.1|FQ446839
EST:     GGTGGAGATGACTCANACACAAATGCTTGCCTTCTTGCTGAAAACTTTAG                         GAGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|349820950|gb|FQ408658.1|FQ408658
EST:     GGGGGAGATGACTCANACACAAATGCTTGCCTTCTTGCTGAAAACTTTAA                         GAGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCCAAGACCATTGATGG
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|110689257|gb|EE065321.1|EE065321
EST:     GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAN                         GGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCCAAGAC-ATTGATGG
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|110730531|gb|EE107719.1|EE107719
EST:     GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAG                         GAGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|71865073|gb|DT014128.1|DT014128
EST:     GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAG                         GGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|161714537|gb|FC062987.1|FC062987
EST:     GAAAACTTTAG                         GGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
genomic: GAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|110698469|gb|EE075999.1|EE075999
EST:     GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAG                         GGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|349808365|gb|FQ405533.1|FQ405533
EST:     GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAG                         GAGTAAAAATATGAAAGCTCGGGTGATTGGATGCCC
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCC
EST: gi|349833359|gb|FQ416737.1|FQ416737
EST:     GGTGGAGACGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAG                         GAGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGG
EST: gi|351034089|gb|FQ448007.1|FQ448007
EST:     GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAG                         GAGTAAAAATATGAAAGCTCCGGTGATTGGAATGCCC
genomic: GGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtaca ... gacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGA-TGCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAAACTTTAGgtgtggtacaggtcaattttgttgataggataatcaagtttctaagggggaactttagttggcgatcagctttgccttcttttattttttctttttttct

- - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggggaa