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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG

Basic information

species Vitis vinifera
transcript Vv02s0025g02740.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
-----------gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagt--ttctctcctaataacatgatgttggtac-------tttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
|| || | ||| || ||||||| | | || | || | ||| | || | | ||| || | | | ||| | | | | || ||| || ||||| || |||||||||||||| || |||||||| ||||| ||||| ||||||
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG

upper sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 3
--gtgagaaacttt----gccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
|| || ||| ||| ||| | || || | || | || || | | | | | |||| | || || | | || || || ||| ||| |||||||| || ||||||||||| ||||| ||||| ||||| ||||| ||||||
gtatgcaaaccttctggaaccaacatgcttgtcttaagttcatgg---ctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctccagCCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAG

upper sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
|| ||| | | | || ||| | || || || ||| | | || ||||| || || | | | | |||| ||||||||| || ||||||||||||||||| || |||||||| || || || ||||||
------------------------gtgagattttcctctactatgcaaagt----ttctgatg--gttagcgactgaggaaaatgat-ttagtcttgtcta-tgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG

upper sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtact---ttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
| | | | || | | || || | | | || | || | ||| | | |||| || || || || | | ||| ||||||||| || ||||||||||||||||| || ||||| || || ||||| ||||||
---------------gtaaggttttttcttgtgtttcatcacattctgactgcaaagttatggttttttagactcaagaggtttgattttagtcctgtctttgttcttagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG

upper sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgagaaactttgccatt---atgatcgttt-tcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
|| || || | ||| ||| | || | ||| | || ||| | | | |||| | | ||| |||| | | |||| | | | ||| ||||||||| || || ||||||||| | || || ||||||||||||||||| ||||||
-ggaattgtttcatacttgcaacgattgttagtgatatgccatagttcttgaat-acggctcggatgaattctggctc----taacttagt-----tactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG

upper sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 3'ss of exon 6
-------gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
||| ||| ||| | | | ||| | || | || || |||||| || | | || | | |||| | | | || | ||||| |||||| || || || ||||||||| | || || ||||||||||||||||||||||||
aagaattttgataaatttt--tagtgacgtagttgt-atgtgaacaatcctggaaattg---cttcaataaggtggttgttctaacacaac--------ttctctatgtttcagTCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAG

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|34416313|gb|CF415067.1|CF415067
EST:     TGCCATCTAAAACAGCCATTGCACCAGTTAACCCTACATTTTTGCCTAGG                         AATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATT
genomic: TGCCATCTAAAACAGCCATTGCACCAGTTAACCCTACATTTTTGCCTAGGgtgagaaact ... tggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
                       taataac  putative branch site (score: 1)
 taataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG