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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttcattatatttgttattcattcatttgtttatcattattgtatatccttttggtgttttctgtaaaattgacacatgttatgttatgtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACACAGCTCAGCCATAATGTAGCAAAGTTCAGATTTGATCTTCCTACTCCCAC

Basic information

species Vitis vinifera
transcript Vv08s0056g01150.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G157263_T01 (Zea mays), 3'ss of exon 1
ttcttcattatatttgttattcattcatttgtttatcattattgtatatccttttggtgttttctgtaaaattgacacatgttatgt-tatgtgcttc-tagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACACAGCTCAGCCATAATGTAGCAAAGTTCAGATTTGATCTTCCTACTCCCAC
    ||||| | ||| || ||| |   |  |   ||     | | |      |    | |||    |  |  | |    ||||   | | | || |   |||| ||||||||||| |||||||||||| | |||||||||||  ||   |  ||||| || |||||||| || |||||||  ||||  || || || || ||
--gctcattcttttttttcttcttctttaggaacatggagctcgcagcctagtcccatttttctcttgtacctcatttgtgttggctgtgtctgttctgtagGATGCCTAGACCCCGAGAACTTCAAGGAGTTCAAACTTGTTGAGAAGAGGCAGCTGAGTCATAATGTTGCCAAGTTCAAGTTTGCGCTCCCAACACCTAC

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 1
ttcttcattatatttgttattcatt-catttgtttatcatt----attgtatatccttttggtgttttctgtaaaattgacacatgttatgttatgtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACACAGCTCAGCCATAATGTAGCAAAGTTCAGATTTGATCTTCCTACTCCCAC
       | | | |   |   ||   | |||| |  |||||     ||  || |  || | || | | ||  ||  ||  |     || |  | ||||||| |||| ||| | ||||| |||||||| |||  |||||||||||| |||||  ||||||| ||||||||||| |||||||||| |||||  || || || || ||
-----tgtaaaactcaatgcacaccacctttggtgttcatttcatgttaaatttggttgttgtatatacttaaagttttccgtcatttcttctgtgtgcttatagGTTGCTTGGACCCAGAGAACTTTAAGGCATTCAAACTTGTTAAGCGTGCACAGCTGAGCCATAATGTTGCAAAGTTCACATTTGCACTCCCAACACCTAC

upper sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 1
ttcttcattatatttgttattcattcatt--tgtttatcattattgtatatccttttggtgttttctgtaaaattgacacatgt-tatgttatgtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACACAGCTCAGCCATAATGTAGCAAAGTTCAGATTTGATCTTCCTACTCCCAC
    ||| |  | |    | |||  | ||  |||| ||   | ||  || |  || | || | | ||  ||| |   ||    | | |  | ||||||| |||| ||| | |||||   |||||| |||   ||||||||||| |||||  ||||||| ||||||||||| || ||||||| |||||  ||||| || || ||
---ctcaatgcactgagcactcagcctttggtgttcattcatgttaaatttggttattgtttctacttcaaagtgttcattcatatcttctgtgtgcttatagGTTGCTTGGACCCATTGAACTTTAAGGTGTTCAAACTTGTTAAGCGTGCACAGCTGAGCCATAATGTTGCTAAGTTCACATTTGCACTTCCAACACCTAC

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|33406972|gb|CF212599.1|CF212599
EST:     GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAG                         GCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC
genomic: GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAGgtctctcacc ... gtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC
EST: gi|351024116|gb|FQ423539.1|FQ423539
EST:     GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAG                         GCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC
genomic: GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAGgtctctcacc ... gtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC
EST: gi|294965698|gb|GW839153.1|GW839153
EST:     GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAG                         GCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC
genomic: GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAGgtctctcacc ... gtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC
EST: gi|351015566|gb|FQ426808.1|FQ426808
EST:     GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAG                         GCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC
genomic: GGCAGTTGTGGCTGGGGCTGCATATTTCTATTCCACCAGGAAACCCAAAGgtctctcacc ... gtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatccttttggtgttttctgtaaaattgacacatgttatgttatgtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACACAGCTCAGCCATAATGTAGCAAAGTTCAGATTTGATCTTCCTACTCCCAC
                        aattgac  putative branch site (score: 3)
                                              tgcttct  putative PPT
              ttttctgtaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttcattatatttgttattcattcatttgtttatcattattgtatatccttttggtgttttctgtaaaattgacacatgttatgttatgtgcttctagGCTGCCTAGACCCTGAGAACTTCAAGCAATTCAAACTTGTCAAGCGCACACAGCTCAGCCATAATGTAGCAAAGTTCAGATTTGATCTTCCTACTCCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - -cattcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacatg