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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggccttgtgacccttttttttttctttttttttttattttatatatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG

Basic information

species Vitis vinifera
transcript Vv17s0000g07780.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G121851_T02 (Zea mays), 3'ss of exon 4
-ggccttgtgacccttttttttttctttttttttttattttatatatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgc-agTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG
    ||  ||| |    | |     |   |  |   |  |  ||| |     | |||  || |  |   |   ||||        |   | || ||  | ||||||||||||||||||||| |||| |||    || ||||| |||||  ||||||| ||||| || || || ||||| ||||||||||||| |||||| | 
atatctactgatctacatctccaattgaatgatgagacatgctatttcc--ctgaatacttctaaaatggtgtaatttaattgattacctcctattgaccagTGTACAAGAAGCACCACCCACCATTTCTTGAAGATGAAGTCTGGCGCCTAGAGAAAATTGGCAAGGAAGGTGCTTTTCACAAGCGTTTGAATAGGGAGAA

upper sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G10040.1 (Glycine max), 3'ss of exon 3
-----ggccttgtgacccttttttttttctttttttttttattttatatatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG
          | | |       | |||    ||||    |   || |  | |  |   |  | |||      |    | ||   |  |||||||| ||  ||||||||||||||||||||| |||||   ||||   || ||||| ||| |||| || || || || || |||||||||||||||||||| |||||| |||||| 
agtaaaattatataatagaacatatttgagcttttcaagtcccttgtcaaaacaagatagggattt-----gaacttagtttgaatgtctgatttttggctgcagTGTACAAGAAGCACCATCCTCCTGGTCTGTCTGATGAAGTTTGGAGATTGGAAAAAATAGGCAAGGATGGAGCTTTCCACAAGCGCTTGAGTCGGGAAAA

upper sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G01860.1 (Glycine max), 3'ss of exon 3
------ggccttgtgacccttttttttttctttttttttttattttatatatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG
           | | |       | |||    ||||    |   || |  | |  |   |  | |||      |    | ||   |  ||| |||| ||  ||||||||||||||||||||| |||||   ||||   || ||||| ||| |||| || || || || || |||||||||||||||||||| |||||| |||||| 
cagtaaatttatataatagaacatatttgagcttttcaagtcacttgtcaaaacaagagagggattt-----gaacttagtttgaatgtct-atttttggctgcagTGTACAAGAAGCACCATCCTCCTAGTCTGTCTGATGAAGTTTGGAGATTGGAAAAAATAGGCAAGGATGGAGCTTTCCACAAGCGCTTGAGTCGGGAAAA

upper sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4
ggccttgtgacccttttttttttctttttttttttattttatatatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG
 ||| ||||  | |   ||  |||| |  |   |    | ||  | |  |  |||    | |   ||     ||| |       || |  |  | | |||| |||||||||||| | || ||  || | |  ||||| || |||||||| || |||||||||||||| || ||||||||||| ||| | | |   | |||
tgccctgtgcacatccattcgttctgtgctgaatgccgtgattaacagaagaaaaatcatatctctatatctaataattgttgttggtcaccttgtacagTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAATCAAGCAAG

upper sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
-ggccttgtgacccttttttttttctttttttttttattttata-tatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG
  |    ||| |    |||||           |        ||  ||  |||||  |||      | ||        |  |  ||   | ||  ||  ||||||||||| |||||| |||| ||  |  |||  ||||| |||||||| || || |||||||| |||||||| ||||||||||||||| | | |   |  | 
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgt--gcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

upper sequence: Vv17s0000g07780.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4
ggccttgtgacccttttttttttctttttttttttattttatatatatgattaaatgtt----ttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG
     ||  |   |||     || |  |       |      |   ||| | |||        | |   ||      ||||       ||||| || | | |||| |||||||||||| | || ||| |  |||  ||||| || |||||||| || |||||||| ||||| || ||||||||||||||| | | |   |    
---tctgccaga-tttccaagttgtgatcagaagaagaaagaagggatggtgaaagcccaacatatctgtatttttgattattgttgttgattactctgttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA

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|71867839|gb|DT016894.1|DT016894
EST:     ACGAGAAGCAAAGACAGAATCATTCATTGTCAGGGATCACCGGGGAGAAT                         TGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAG
genomic: ACGAGAAGCAAAGACAGAATCATTCATTGTCAGGGATCACCGGGGAGAATgtgagtactc ... ctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG
                                    ctctgat  putative branch site (score: 4)
                                          tttctgttt  CT-rich tract
     ttaaatgttttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggccttgtgacccttttttttttctttttttttttattttatatatatgattaaatgttttttcataagaaaaattacgacctctgatttctgtttgcagTGTACAAGAAGCACCACCCTCCATCTCTGATGGACGAAGTGTGGCGATTAGAGAAGATTGGAAAAGATGGAGCTTTCCACAAGCGTTTGAGTAGGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- ccttgtg
- - - - - ccctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgacctc