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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatgatgcagtaatagttctccttacttcagcaatacatagtgatttttattgacacctataaattccaatttacactttcaattgtttgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCTGGAGGAGGCTAGAGATCGCTGGGAGAAGCATGGCATCAAAGTTGTTGTT

Basic information

species Vitis vinifera
transcript Vv16s0050g00600.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G25200.1 (Glycine max), 3'ss of exon 13
aatatgatgcagtaatagttctc-cttacttcagcaa--tacatagtgatttttattgacacctataaattccaatttacactttcaattgtttgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCTGGAGGAGGCTAGAGATCGCTGGGAGAAGCATGGCATCAAAGTTGTTGTT
  |  ||   ||| ||  ||  | | ||  |   | |   | | | | ||   | || || |   || || |  | | |    ||    || || ||    ||||||||||| ||||||||||| ||| | |  ||||| ||||||| |||| | ||||||||||||||||| ||||||| |||||| |||||||| || |||
--ttagagaaagtcatttttgacacatatattgtccagtcaaaaaataatagctctt-accctattacatccttaataaatggttatgctgattcttggacagGGCTTGGGCAGAGGATGAGGCCAAACGAGTGAGAGAGCAAGCAATAGCCTTAGAGGAGGCTAGAGATCGTTGGGAGAGGCATGGAATCAAAGTGGTAGTT

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G30160.1 (Glycine max), 3'ss of exon 9
aatatgatgcagtaatagtt--ctccttacttcagcaatac-atagtgatttttattgacacctataaattccaatttacactttcaattgtttgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCTGGAGGAGGCTAGAGATCGCTGGGAGAAGCATGGCATCAAAGTTGTTGTT
  || ||   ||| ||  ||  | | |   ||   || | | | | | ||   | ||  |   | || || |  | | |    ||   ||| || |     ||||||||||| ||||| ||||| ||| | |  ||||| ||||||| |||| | ||||||||||||||||| ||||||| |||||| |||||||| || |||
--taagagaaagtcatttttgacacatatattgtccagtcctaaaataatagctgttagcgtat-tacatccttaataaatggttatgttgattctcggacagGGCTTGGGCAGAGGACGAGGCCAAACGAGTGAGAGAGCAAGCAATAGCCTTAGAGGAGGCTAGAGATCGTTGGGAGAGGCATGGAATCAAAGTGGTAGTT

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G52410.2 (Arabidopsis thaliana), 3'ss of exon 10
aatatgatgcagtaatagttctccttac---ttcagcaatacatagtgatttttattgacacctataaattccaatttacactttcaattgtttgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCTGGAGGAGGCTAGAGATCGCTGGGAGAAGCATGGCATCAAAGTTGTTGTT
| |   |  ||  ||   || |  | |    |    |||  || |   ||     || |   ||  | |||   ||||||  |||  | | ||  || |  |||| ||||||| ||||||| || | ||| |||||||||||||||||||  || || || |||||||  || ||||||||| ||||| | |||||  |||||
agtgaaactcaaaaacttttatattgaaaaatgtgacaaatcaaacatatgagagtttagctcttcagatt---atttactgttttgagttttgtttttgaagGGATTGGGCTAAGGATGAAGCGAGAAGAGCAAGAGAACAAGCAAAAGTGCTAGAAGAAGCTAGAGGACGTTGGGAGAAGTATGGCCTAAAAGTGATTGTT

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|110361260|gb|EC924722.1|EC924722
EST:     CGATTACAATATGAGCTGGAGGTTGAGAGGAAAGCCTTGTCTATGGCCAG                         GGCTTGGGCTGAGGATGAGGCAAAAAGAGCAAGAGAACAAGCAAAAGCCCT
genomic: CGATTACAATATGAGCTGGAGGTTGAGAGGAAAGCCTTGTCTATGGCCAGgtaagaatca ... tgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCT
EST: gi|110689004|gb|EE067895.1|EE067895
EST:     CGATTACAATATGAGCTGGAGGTTGAGAGGAAAGCCTTGTCTATGGCCAG                         GGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCT
genomic: CGATTACAATATGAGCTGGAGGTTGAGAGGAAAGCCTTGTCTATGGCCAGgtaagaatca ... tgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCT
EST: gi|110700815|gb|EE077801.1|EE077801
EST:     CGATTACAATATGAGCTGGAGGTTGAGAGGAAAGCCTTGTCTATGGCCAG                         GGCTTGGGCTGAAGATGAAGCAAATATGGCAAGAGAACAACCAAA-GCCCT
genomic: CGATTACAATATGAGCTGGAGGTTGAGAGGAAAGCCTTGTCTATGGCCAGgtaagaatca ... tgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttattgacacctataaattccaatttacactttcaattgtttgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCTGGAGGAGGCTAGAGATCGCTGGGAGAAGCATGGCATCAAAGTTGTTGTT
     tattgac  putative branch site (score: 2)
               tataaattccaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatgatgcagtaatagttctccttacttcagcaatacatagtgatttttattgacacctataaattccaatttacactttcaattgtttgttatctagGGCTTGGGCTGAGGATGAGGCAAAAAGGGCAAGAGAACAAGCAAAAGCCCTGGAGGAGGCTAGAGATCGCTGGGAGAAGCATGGCATCAAAGTTGTTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -gatgcag
- - - - - - - - - - - - - - -tcagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acaccta