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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgattcttattataatcagctaagcttaagaccaagttaattatgatcagacatgcaaaaaaactgtgtcaatatctactaattctcttgacacattcgttatgtctgtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04250.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 9
gtacttgattcttattataatcagctaagcttaagaccaagttaattatgatcagacatgcaaaaaaactgtgtcaatatctactaattctcttgacacattcgttatgtctgtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG
               | |||||  |  | |    |  ||  |||||| | |||   | |||  |  |   |||     ||| | |  ||       ||  ||| |  | | |||| |    ||| || || ||||| ||||||||||| |||||  |||| ||||||||||| || |||| ||||||||||||    ||||| ||  |||||
------------gtgtgtaatcttcatatcact-gttcattttaattgtaatctaccgtgcttactattcgtgc----atcaatttgtttctgcttcatcttcatcttctttgtgaa----gGTTCCGTGCGTTGCAGTTGTTGAGAACATGTGCTACTTCGATGCTGATGGAAAACGATTTTACCCATTTGGGCAAGGTTCTGGAGCTCAG

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G129208_T01 (Zea mays), 3'ss of exon 8
gtacttgattcttattataatcagctaagcttaagaccaagttaattatgatcagacatgca-aaaaaactgtgtcaatatctactaattctcttgacacattcgttatgtctgtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG
                         |  |   |  |     |  ||||| |  || |  ||  | ||| ||      | ||  |||| ||    |     || |  |   ||||| |  | |||| || |||||||| ||||| ||||| |||||  | |||||||||||||| || || ||||||||||||||    ||||| ||  |||||
------------------------gtgtgtccacaatgtgatgcattat-acaagtctagcgtataaatctaaccttacattgactagtttctgt-----atcctct---tctgt-cgccaagGTTCCTTGTGTTGCGGTTGTAGAGAACATGTGCTATTTTGATGCTGATGGAAAACGTTATTACCCATTTGGACAAGGTTCTGGAACTCAG

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------------gtacttgattctt--attataatcagctaagctta-agaccaagttaattatgatcagacatgcaaaaaaactgt---gtcaatatctac----taattctcttgacacattcgtta------tgtctgtgcatcc---agGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG
                                                        | ||||  | ||  ||||||   |  ||    || | |   |  ||  |||    | |  ||  |||  | |     ||||  || ||     || |||  |||| || | | ||       ||| |||  || |   |||| || |||||||||||||| |||||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||| ||||||
gtggttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattatatatatatatatatatatatatatatatatatatatataattgtgaaagtatttgctagtcataatttaagtcatacttcatttgatacttacatttattttttgtttgttaatgcgtaagGTGCCTTGTGTTGCTGTTGTGGAGAATATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------gtacttgattcttattataatcagctaagcttaagaccaagttaattatgatcagacatgcaaaaaaactgtgtcaatatctactaattctcttgacacattcgttatgtctgtgcatcca---gGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG
                                                                       |  || || |||  | |  | |  ||   |||| |  || |     |  ||  |  |  || |     | ||    ||| | |   |  |  | | |  |   ||  ||||||  || ||   ||| || |||||||||||||| ||||| |||||||| |||||||||||||| || |||||||||||||||||||| |||||||| ||||||
gtgcttcttctacaatttgaagacataactattccattttattgttttcaatcccatgcttgtgttttgcattttttatccttcctctgtttatatatatttaaaaaaaaatgtgaaagtatttgctagtcatacttcttttgattctattttcatttaatacttatatttagttttcgtctgttaatgcataagGTGCCTTGTGTTGCTGTTGTGGAGAACATGTGTCATTTTGATGCTGATGGAAAACGATATTACCCATTTGGCAGAGGTTCAGGTTCTCAG

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G24430.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------gtacttgattcttattataa----tcagctaagcttaagaccaagttaattatgatcagacatgcaaaaaaactgtgtcaa-tatctactaattctcttgacacattc---gttatgtctgtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG
           || |  || | | || ||||    ||   |    || | |   || |  | |   |            ||  |||   |||  |  ||  || |  |  ||   |||    |||  || |        |||| || || ||||||||||| ||||||||||| |||||||| |||||||| || || |||||||| ||||| |  |||||||| ||| ||
gttatttccctgttccagactttgatcataaactctcctttttcttttatatggagcttgtgaacttgtttttcttctcaactctgcaacaaacagatatgaacttccgagatttatttcctgtttggttttacggagtagGTGCCTTGCGTTGCTGTTGTGGAGAATATGTGCCACTTTGACGCTGATGGGAAACGTTATTACCCTTTTGGGAAAGGTTCAGGTTCTGAG

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|32267762|gb|CD716725.1|CD716725
EST:     TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAG                         GTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC
genomic: TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAGgtacttgatt ... gtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC
EST: gi|110718478|gb|EE095359.1|EE095359
EST:     TAGCCTTCATTGATGTTGCGAAAGGAGTCCGTATGTTTTCAAAACTTAAG                         GTCCCCTGTGTTGCTGTCGTTGAGAATATGTGCCACTTTGATGCTGATGGC
genomic: TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAGgtacttgatt ... gtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC
EST: gi|30328118|gb|CD011380.1|CD011380
EST:     TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAG                         GTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC
genomic: TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAGgtacttgatt ... gtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC
EST: gi|32269673|gb|CD718832.1|CD718832
EST:     TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAG                         GTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC
genomic: TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAGgtacttgatt ... gtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC
EST: gi|294966635|gb|GW839626.1|GW839626
EST:     TAGCCTTCATTGATGTTGCGAAAGGAGTCCGTATGTATTCAAAACTTAAG                         GTCCCCTGTGTTGCTGTTGTTGAGAATATGTGCCACTTTGATGCTGATGGC
genomic: TAGCCTTCATTGATGTTGCAAAAGGAGTCCGTATGTTTTCAAAACTTAAGgtacttgatt ... gtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtgtcaatatctactaattctcttgacacattcgttatgtctgtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG
        aatatctactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgattcttattataatcagctaagcttaagaccaagttaattatgatcagacatgcaaaaaaactgtgtcaatatctactaattctcttgacacattcgttatgtctgtgcatccagGTCCCCTGTGTTGCTGTTGTTGAGAATATGTGTCACTTTGATGCTGATGGCAAGCGATATTACCCATTTGGCAGGGGTTCAGGCTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT