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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcagctactttgttttttatctcaaaaatgaaaagaggccaaacccctgaaggaaaactaacttgaattgcccgtaacattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC

Basic information

species Vitis vinifera
transcript Vv18s0089g00930.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g00930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g65560.1 (Oryza sativa), 3'ss of exon 3
catcagctactttgttttttatctcaaaaatgaaaagaggccaaacccctg---aaggaaaactaacttgaattgcccgtaacattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC
    |     |    |  |   ||  || ||   || |   || |   |||   ||  || |     | ||| || ||   |  |    | | ||||   ||||| ||||||||  | || |||||| |||  |  || || |||||||||||||||||||| |||||||| ||||||||||||||  | || |||||| | |
-tcgaagcgttgaaatgctaggctttaacatactaacattacatagttctgtttaattaacatatggtagaactgacct--atttgggatatatttctttcagATCTACAGAGAAGCCACTGGAACTTCTTCTGCTGATGATACAGGCTATGGAGATCCTGTGCAGAAGGCTGAAGCAATGGCTTTTCGCCGAGCTTGTACCC

upper sequence: Vv18s0089g00930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G005061_T03 (Zea mays), 3'ss of exon 1
catcagctactttgttttttatctcaaaaatgaaaagaggccaaacccctgaaggaaaactaacttgaattgcccgtaacattatttgt-ctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC
       | |  |  ||||  | | | | || | |   |  || | |    |   | |    | |   | ||       |  | | ||| || || | ||||| || |||||| | || ||||||||||  || || || ||| ||||||| |||||  |||||||||| ||||| ||||||||  | |||||||||||||
ttctgagtgcagtagtttt-gtttaacatataatatatgatcagaactaacataaatagtgtattgacaatgttatctgctctctctgttctctctatcagATCTATAGAGAGGCTACTGGAACTGCTTCTGTTGATGATACAAGCTATGGTGATCCCATACAGAAGGCAGAAGCTATGGCTTTTCGTCGTGCTTGTGCAC

upper sequence: Vv18s0089g00930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G36860.1 (Glycine max), 3'ss of exon 3
---cat-cagctactttgttttttatctcaaaaatgaaaagaggccaaacccctgaaggaaaactaacttgaattgcccgtaacattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC
    ||  || ||  | ||  || |  |  ||||| |  |||                  |  ||  ||| | |  ||||  |  |    | | ||||  | |||| |  || || ||||| || ||||||| |||||| |||||| | ||||||||||||||||||||||| ||||||||||||||  |  | ||||||||||
gaaaatgtagtta--tggtgattgagttggaaaattagcagattttgttagttcctcttcattctgtctt-attgacccggtaagtcccatttatttct-ctagATATTTAGGGAATCAACTGGTACTGCTTCAGTAGACGACACAAGTTATGGAGATCCTGTACAGAAGGCAGAAGCAATGGCTTTTCGTAGAGCTTGTGCAC

upper sequence: Vv18s0089g00930.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G71310.1 (Arabidopsis thaliana), 3'ss of exon 3
-catcagctactttgttttttatctcaaaaatgaaaagaggccaaacccctgaag-gaaaactaacttgaattgcccgtaa-cattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC
 | |    |||||| ||    || | |    |  |  |        |   | |   | |  || |  | | ||||   ||| |||| |||   | |   | |||| |  || || |||||||| ||  | |  ||||| |||| ||||||||| ||| |||| || ||||||||||||||||| ||  | ||||| |||||| 
tccttgcatactttcttgagcatattatgttttcattg---ttttgcttgtaacttgtacgctgaaatcatttgctaataatcatttttttggtgttgtcaagATATTTAGGGAATCAACAGGTACCACATCTGTAGATGACAAAGGCTATGGTGATGCTGTGCAAAAGGCGGAAGCAATGGCATTTCGCCGTGCGTGTGCAA

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|27585237|gb|CB007932.1|CB007932
EST:     AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAG                         ATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
genomic: AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAGgtaatttttt ... tttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
EST: gi|30329758|gb|CD013020.1|CD013020
EST:     AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAG                         ATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
genomic: AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAGgtaatttttt ... tttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
EST: gi|161717593|gb|FC066897.1|FC066897
EST:     AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAG                         ATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
genomic: AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAGgtaatttttt ... tttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
EST: gi|22011015|gb|BQ796049.1|BQ796049
EST:     AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAG                         ATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
genomic: AATCTGTATCTGTTGTTTACCGTGTAACACTATATGGGACTGATGCAGAGgtaatttttt ... tttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
EST: gi|32457473|gb|CD798647.1|CD798647
EST:     GACTGATGCAGAG                         ATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA
genomic: GACTGATGCAGAGgtaatttttt ... tttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccctgaaggaaaactaacttgaattgcccgtaacattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC
                                    ttatttgtctttcc  CT-rich tract
                               taacattattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcagctactttgttttttatctcaaaaatgaaaagaggccaaacccctgaaggaaaactaacttgaattgcccgtaacattatttgtctttccaccagATGTACAGAGAGTCAACAGGAACTGCTTTAGTAGAGGACACAGGCTATGGAGATCCTGTACAGAAGGCGGAAGCAATGGCTTTCAGGCGTGCTTGTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
catcagc
- - - - - - - - - - - - caaaaat
- - - - - - - - - - - - - - - -gaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattgcc