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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttctagacttcagattctagttttaaataaagcatccactcaggttgaaggtaatttttgttttttaattcttttgtttgatatttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATCTTGATACTTGATACACATGCTGAAGTTTTTGTTTGGGTTGGTCAGACTG

Basic information

species Vitis vinifera
transcript Vv08s0007g08690.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 18
gtgtgttctagacttcagattctagttttaaataaagcatccactcaggttgaaggtaatttttgttttttaattcttttgtttgatatttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATCTTGATACTTGATACACATGCTGAAGTTTTTGTTTGGGTTGGTCAGACTG----------------------------
|| ||||   |  ||  ||||  |  |  ||||    | |    ||  ||      |  |  || ||||  |||  | |        | ||   | ||||||   ||||| | ||| |||   ||||||||||||||||| || || ||  ||||||||||||||||   ||| |||||||||||| | ||||||  ||                            
gtttgtttctgtatt--gatttga--tccaaattggtctt--gttccagt----aatcttgctttttttaaaataatctgaaagctcacttgtacgcaggttactgaaattttcaatttttcacaagATGATCTGTTGACCGAAGACATGATGATACTTGATACACACTGTGAGGTTTTTGTTTGGATGGGTCAGTGTGTGGAGACAAAAGAAAAACAGAAAGCATT

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 17
gtgtgttctagacttcagattctagttttaaataaagcatccactcaggttgaaggtaatttttgttttttaattcttttgtttg-atatttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATCTTGATACTTGATACACATGCTGAAGTTTTTGTTTGGGTTGGTCAGACTG
                       || ||   ||| | | | || |      || | |  | |   | || ||    | ||      ||  |      ||||||||||| || |||||||||  ||||||||| || |||||||||||||| |   | || || || ||||||||||||||||| |||||||||||   ||
--------------------gtgagatt---atacaactttcattactcgagatgctgttctgcatattctacccttcttaacaatatgctctgcaacagGTTGAGGAGATTTACAACTTTGCTCAAGATGACCTCTTGACTGAGGATATATATTTCCTAGACACCCATGCTGAAGTTTTTGTCTGGGTTGGTCAATGTG

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgtgttctagacttcagattctagttttaaataaagcatccactcaggttgaaggtaatttttgttttttaattcttttgtttgatatttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATCTTGATACTTGATACACATGCTGAAGTTTTTGTTTGGGTTGGTCAGACTG
              | ||| | |||    | ||  | | |    | |   | ||| |   ||   | ||||||    ||   |||         | |||||||| || ||  |||||||| |||||||||| || ||||| ||||| ||     |||| ||||| ||||||||||||||||| |||||||||||   ||
-------------gtgagaatttagaaaaatatccaacgttttttta---tcaagatgtgttgcatgttttaacatattaccttg---------cacagGTTGAAGAGATTCACAACTTTGATCAAGATGACCTCTTGACGGAGGAAATGCATTTACTAGATACTCATGCTGAAGTTTTTGTCTGGGTTGGTCAATGTG

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|71870008|gb|DT019063.1|DT019063
EST:     CTCATTCAACAAAGGGAAGTTTGAG                         GTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATC
genomic: CTCATTCAACAAAGGGAAGTTTGAGgtgtgttcta ... ttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATC
EST: gi|71870041|gb|DT019096.1|DT019096
EST:     CTCATTCAACAAAGGGAAGTTTGAG                         GTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATC
genomic: CTCATTCAACAAAGGGAAGTTTGAGgtgtgttcta ... ttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggttgaaggtaatttttgttttttaattcttttgtttgatatttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATCTTGATACTTGATACACATGCTGAAGTTTTTGTTTGGGTTGGTCAGACTG
                                            tttcatctc  CT-rich tract
            taatttttgtttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttctagacttcagattctagttttaaataaagcatccactcaggttgaaggtaatttttgttttttaattcttttgtttgatatttcatctcagGTTGAGGAAATCTACAACTTTAATCAAGATGATCTGTTGACTGAGGATATCTTGATACTTGATACACATGCTGAAGTTTTTGTTTGGGTTGGTCAGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG