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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaacttcccacaggaagactccaatatttgcatcaaatttgtactggttaaaaaaagtcatacttctctgatgagagtatacttttattattttcaaac...

Basic information

species Vitis vinifera
transcript Vv09s0002g00100.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 14
GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaa------cttcccacaggaagactccaatatt--tgcatcaaatttgtactggt----taaaaaaagtcatacttctctgatg----agagtatacttttattattttcaaac-----
 || || ||| ||||||| ||||||||||| || ||||| || ||||| ||||| ||||| ||||| || |||||||||||||| ||| || | ||  ||||||      ||  |||  |      |   | ||   ||||||| | ||||| || |    |     |  ||| | |  |    |     ||  ||     |||| | || |  |      
AGGGTTCTATCTAGCTGGTGACTACACAAAGCAGAAATATTTGGCTTCGATGGAGGGTGCAGTTCTATCTGGGAAGCTTTGTGCTCAGTCTGTAGTGGAGgtaaacgctgctctccatggttctgtttgtacatagatgcatcagacttgtattgttgtcttggtgcagttcacaatgattcagttttgtaggctaatgagttatcacttgctgatttcag

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G410515_T01 (Zea mays), 5'ss of exon 14
GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaac------ttcccacaggaagact-----ccaatatttgcatcaaatttgtac-tggttaaa-----------aaaagtcatacttctctgatga-gagtatacttttattattttcaaac
 || || ||| ||||||| || |||||||| || |||||| | ||||| ||||||||||| || || || ||||||||||| || ||| | |||||  ||||||       | | ||| |     ||        |||   |||||| |||| |   | |||  |           |  |  |||  ||  | | | | || |  || |||| |  || ||   
AGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAATACCTGGCTTCCATGGAAGGTGCAGTCCTATCCGGGAAGCTTTGCGCCCAGTCCATTGTGCAGgtaaataaatatactcaccgtggtcctggttgtgcataaaagcatcagatttctgtgttgttggatttatttcggtatgatacatgttttgcagctaatgaattaacatttactgcttccag--

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA18G00720.1 (Glycine max), 5'ss of exon 13
GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaacttcccacaggaagactccaatatttgcatcaaatttgtactggttaaaaaaagtcatacttctctgatgagagtatacttt-tattattttcaaac
 || || ||||||||||| || ||||||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||||||||||||| ||||||  ||  |||  || |   | || |      ||    |  | | |  || ||| || ||| |      ||    |  | |||  || | || | | | 
AGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAATATTTAGCTTCAATGGAAGGCGCTGTTCTTTCTGGGAAGCTTTGTGCACAGGCTATTGTACAGgtaaaatctgacacaaaaatatctatgtaactcgcagcaatacattagc-aagaaatgtgataatctatatatacatgctttcttggtaattttgtgagag

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 13
GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaacttcccacaggaagactccaatatttgcatcaaatttgtactggttaaaaaaagtcatacttctctgatgagagtatacttttattattttcaaac----
 || || ||||||||||| || ||||||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||||||||||||| ||||||  ||   ||  || |   |  ||| |   |||    |  | | |  || ||| || ||  |      || |  |  | |||   |||||||   |     
AGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAATATTTAGCTTCAATGGAAGGCGCTGTTCTTTCTGGGAAGCTTTGTGCACAGGCTATTGTACAGgtaaaatctgtcacaaaaatatc--tatgtaactcagcgattcattagc-aagaaatgtgattatctatatataaatgctttctta-gttattttgtgagagaa

upper sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 14
GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaa-------cttcccacaggaagactccaatatttgcatcaaattt--gtactggttaaaaaaagtcatacttctctgatgagagtat---acttt-tattattttcaaac----------------------------------------------------
 || || || |||||||| || ||||||||||| || ||||||||||| |||||||| ||||| || || || ||  | ||  | ||| |||||||  ||||||       ||| |||    || | |  |  | |  | |     |    | || |||  || |  ||     |  | | |  |  ||    | ||| | | | | | | ||                                                    
AGGATTCTACTTAGCTGGAGATTACACAAAACAGAAGTACTTAGCTTCCATGGAAGGCGCTGTCCTCTCTGGCAAATTCTGCTCTCAGTCTATTGTTCAGgtaaacacaagcttgccattcaaatagttaaccagtaaccttgttctctgtttcttgttggaatatatcgccaataaccggtcggtttacctgattttgtctcactattatactgttccggttatgtagagaaattgctaaagtcagaatttactggttatacag

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|45771660|gb|CN007512.1|CN007512
EST:     TGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAG                         GACTATGAATTGCTTGTTGCTCAGGGAGAACAAAAGTTGGCCGAGGTCAGC
genomic: TGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaacttccc ... caacatacagGACTATGAATTGCTTGTTGCTCAGGGAGAACAAAAGTTGGCCGAGGTCAGC
EST: gi|352778350|gb|FQ465660.1|FQ465660
EST:     TGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAG                         GACTATGAATTGCTTGTTGCTCAGGGAGAACAAAAGTTGGCCGAGGTCAGC
genomic: TGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaacttccc ... caacatacagGACTATGAATTGCTTGTTGCTCAGGGAGAACAAAAGTTGGCCGAGGTCAGC
EST: gi|110392879|gb|EC957437.1|EC957437
EST:     TGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAG                         GACTATGAATTGCTTGTTGCTCAGGGAGAACAAAAGTTGGCCGAGGTCAGC
genomic: TGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaacttccc ... caacatacagGACTATGAATTGCTTGTTGCTCAGGGAGAACAAAAGTTGGCCGAGGTCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAATACTTAGCTTCAATGGAAGGTGCTGTTCTGTCAGGGAAGCTTTGTGCACAGGCTATTGTAAAGgtaacttcccacaggaagactccaatatttgcatcaaatttgtactggttaaaaaaagtcatacttctctgatgagagtatacttttattattttcaaac

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagagta