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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggatctttgtgtttttttaacttgttcagatgtcttttagcatcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC

Basic information

species Vitis vinifera
transcript Vv14s0006g02020.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
gaggatctttgtgtttttttaacttgttcagat-gtcttttag--catcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC
|   | |   |||||  |  ||||| |||   | |||| |||   ||  | |  |||||||  |   | |  ||  |   |||  || |    |||  ||||||| || ||||||||||||||||| ||||||||||| || ||||||||||||||||||||||| ||  |||| || || ||||| |||||| |||||||  
gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaacactgagtaagcttc-ctgttttcgtgatact--tgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G145854_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------------gaggatctttgtgtttttttaacttgttcagatgtcttttagcatcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC
                                                                                        |   ||| || || | || ||  |  || |||   |    ||  | || |  | | ||||    | | || |  |   |   ||| ||   |  ||||||||||| |||||||||||||| || ||||||||||| || ||||||||||||||||||||||| ||  ||||||| |||||||| |||||| |||||||  
gtttgtttattctccatttattttacaatttggatttttgtgtttttttttgtattcatgtgacctactgcttcgctatgtatcattagttcatcattttgctattctatatctttgagaaaccaa--agattattatgttaatatgtttagtgaaca-tcacttttcctttttcttttcc-ttgcagGACATTAATGAGGAATGGATTTCGGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAATGACCCTATGATCCGTGGTCCTGATGGCA

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G126038_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------------------gaggatctttgtgtttttttaacttgttcagatgtctttta-gcatcttttactgaaatgtaagat-catcaat---ttcagctggc-----tttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC
                                                                                     | | ||| |||  ||  ||||    | |   || ||||| |   |    ||| |   || |||  |   |||||   || || |  |     ||| |       ||||||||||| ||||||||||||||||| || || ||||| || |||||||||||| |||||||||| ||  ||||||| |||||||| |||||| |||||||  
gttggtttattctccatttctgttacaattttgacttttgtgtttgttttgttggtggggtattcatgtgtcctaatgcttcgtggtgtatcattgacttcatttagtccgcttctatatctttgataaaaaggttattatcatataaattatgtcaatatgtttagttaacaccactttccctgttcattgcagGACATTAATGAGGAATGGATATCGGATAAGACACGATTTTGTTATGATGGTTTGAAGAGGCAAAGACTAAATGACCCTATGATCCGTGGTCCTGATGGCA

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 3
----------gaggatctttgtgtttttttaacttgttcagatgtcttttagcatcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC
           | ||        | || |||    |   ||| ||    | || |||||  |   | | |   ||  | ||    |||| | | ||||   |  ||||||||||||||||| |||||||| ||||||||||| || || |||||||||||| |||| ||||||||||||||||| || |||||||||||| |||||||||
tctaaaaagaaaagaaaaaaaaatcttcttagggggagaagaggt----tggcttcttt--ccatagtttgctatttttaa----agcttgttctgcttgcccattgcagGACATAAATGAAGAATGGATTTCAGACAAAACCCGCTTTTGTTATGATGGTTTGAAAAGGCAGAGGTTAAATGACCCCATGATTCGTGGTTCTGATGGAC

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 3
----------gaggatctttgtgtttttttaacttgttcagatgtcttttagcatcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC-
           | ||         || ||     |    ||| ||    | || |||||  |   | | |   ||  | ||    |||| | | ||||   |  |||||||| |||||||| |||||||| || || ||||| || || |||||||||||| |||| ||||| |||||||||||||| ||||| |||||| ||||||||| 
tttttccaaaaaagaaaaaaaaacttcttagggataga-agaggt----tggcttcttt--ccatagtttgctatttttaa----agcttgttctgcttgcccattgcaggAGATAAATGAAGAATGGATTTCGGATAAAACCCGCTTTTGTTATGATGGTTTGAAAAGGCAAAGGTTAAATGATCCCATGATACGTGGTTCTGATGGACG

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 3
gaggatctttgtgtttttttaacttgttcaga-tgtcttttagcatcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC
       | |||  |  |||   |     | | | | ||| |   | |||| ||| |   | |  |  | ||| |                 ||  | ||||| ||||| || ||||||||||| |||||||| || ||||||||||| || ||||| || || ||| | |  || |||||||| || | | | |||||||
------gtatgtaatgcttttgttcaaaaacactatttttaaaagtattttgctggatgttgaacttgtgaatgtt----------------cttattcagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC

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|56409648|gb|CX017900.1|CX017900
EST:     TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAG                         GACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
genomic: TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAGgtagactaag ... actgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
EST: gi|110698529|gb|EE076131.1|EE076131
EST:     CTGAGGTTATGCCTATTCTCCCACGTTTGAATGAG                         GACATAAATGAGGAATGGATATCAGACAAAACACCTTTCTGTTATGATGGT
genomic: CTGAGGTTATGCGTATTCTCCCACGTTTGAATGAGgtagactaag ... actgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
EST: gi|110719363|gb|EE097252.1|EE097252
EST:     TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAG                         GACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
genomic: TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAGgtagactaag ... actgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
EST: gi|110693407|gb|EE069609.1|EE069609
EST:     TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAG                         GACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
genomic: TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAGgtagactaag ... actgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
EST: gi|294967076|gb|GW839951.1|GW839951
EST:     TGATAGCACAGGTCCTGAGGTTATGCGTACTTCTCCCACGTTTGAATGAG                         GACATAAATGAGGAATGGATATCAGACAAAACACGTGTCTGTAATGATGGT
genomic: TGATAGCAGAGGTCCTGAGGTTATGCGTA-TTCTCCCACGTTTGAATGAGgtagactaag ... actgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
EST: gi|110699198|gb|EE075987.1|EE075987
EST:     TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAG                         GACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
genomic: TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAGgtagactaag ... actgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
EST: gi|110699724|gb|EE076975.1|EE076975
EST:     TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAG                         GACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT
genomic: TTGATAGCAGAGGTCCTGAGGTTATGCGTATTCTCCCACGTTTGAATGAGgtagactaag ... actgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC
         aaatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggatctttgtgtttttttaacttgttcagatgtcttttagcatcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctga