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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaaattcagcaaaataacaatatttacatcagtttcttgctgcagttgtttgtactactaaccataaggattgggtttttccttatttttatatcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCTGCAAGTGAACTTTCACAGCATATCAG

Basic information

species Vitis vinifera
transcript Vv14s0108g01560.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01560.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G06040.1 (Glycine max), 3'ss of exon 11
ttaaaaattcagcaaaataacaatatttacatcagtttcttgctgcagttgtttgtactactaaccataag--gattgggtttttccttatttttat---atcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCTGCAAGTGAACTTTCACAGCATATCAG
     || |  | | | |      | | | ||||  || ||||   | | | | |||  |   |   | |     ||   | ||| ||| ||| |||   |||||||||||||||||||||||||||||||||||||||||||  |||||||||| ||||||||| | ||||| ||||||||
--gttaacttcgtacatttttt-cagtaagatcatatttttgca--aatggatggtaaaaaatattgttaatttgttatttatttacttgtttatatttaatcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAGATGCTTATTCCAGCAAGTGAATTGTCACAACATATCAG

upper sequence: Vv14s0108g01560.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G03490.1 (Glycine max), 3'ss of exon 11
ttaaaaattcagcaaaataacaatatttacatcagtttcttgct-gcagttgtt-tgtactactaaccataaggattgggttt--ttccttatttttatatcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCTGCAAGTGAACTTTCACAGCATATCAG
     ||||    | |||      | | |  |||| || ||||  |  | || |    | || |    ||  |  ||   |||  ||  |||| |||| ||||||||||||||||||||||||| |||||||||||||| ||  |||||||||| ||||||||| | ||||| ||||||||
---ttaatttcctacaattttttcagtaaggtcagatttttgcaagtggatgctacaaaatattgttaatttgttttttatttggttgtttatgttta-atcagGTTGTTTTTGTCCCTGATTATAATGTCAGTGTTGCCGAGATGCTTATTCCAGCAAGTGAATTGTCACAACATATCAG

upper sequence: Vv14s0108g01560.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------------ttaaaaattcagcaaaataac--aatatttacatcagtttcttgctgcagttgtttgtactactaacca--taaggattgggtttttccttatttttatat-cagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCTGCAAGTGAACTTTCACAGCATATCAG
                             |   |   |||     |||||  || || | ||  | ||   || |       | |||     |   ||  ||   ||| |   | |   ||  |  | ||  ||||| | ||||| ||||||||||||||||||||||||||| |||| ||||| |||||||| ||||| ||||| |||||
gtatatatctacttacgttcttgtattagtcgtattctcaagcgtataacggaaaatctgcaataattatctggtttttgcatctgtggagattggcacttactaattagaagtgt---taactaaacatgtagGTTATCTTTGTTCCTGATTACAATGTCAGTGTTGCTGAATTGCTCATTCCAGCAAGTGAGCTTTCTCAGCACATCAG

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|161707864|gb|FC055660.1|FC055660
EST:     ATGTTGGGACTACAGTAAATCATGATTCAGAAATAGGTGATTTGCTGAAG                         GTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCT
genomic: ATGTTGGGACTACAGTAAATCATGATTCAGAAATAGGTGATTTGCTGAAGgtatgaagta ... tttatatcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCT
EST: gi|87586833|gb|DY474947.1|DY474947
EST:     ATGTTGGGACTACAGTAAATCATGATTCAGAAATAGGTGATTTGCTGAAG                         GTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCT
genomic: ATGTTGGGACTACAGTAAATCATGATTCAGAAATAGGTGATTTGCTGAAGgtatgaagta ... tttatatcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttgtttgtactactaaccataaggattgggtttttccttatttttatatcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCTGCAAGTGAACTTTCACAGCATATCAG
             tactaac  putative branch site (score: 0)
                                 tttttccttattttta  putative PPT
                                 tttttccttattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaaattcagcaaaataacaatatttacatcagtttcttgctgcagttgtttgtactactaaccataaggattgggtttttccttatttttatatcagGTTGTTTTTGTCCCTGATTACAATGTCAGTGTTGCTGAACTGCTTATTCCTGCAAGTGAACTTTCACAGCATATCAG

-taaaaat
- - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - -tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggattgg