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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgaggcagtacccccttgtctgcaattttttagtttgtaaagatcctttttgttagtgcattgtggatatgtttgcaaatacaacacacacatacaaaagtgtgggcttacaaattgatggtgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAGATTACATCAGACACACTGAGGAACTTGATGGATATGAAAGCAAACTTGG

Basic information

species Vitis vinifera
transcript Vv05s0049g01180.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 6
gtaatttgaggcagtacccccttgtctgcaattttttagtttgtaaagatcctttttgttagtgcattgtggatatgtttgcaaatac-aacacacacatacaaaagtgtgggcttacaaattga---tggtgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAGATTACATCAGACACACTGAGGAACTTGATGGATATGAAAGCAAACTTGG
                           | |||     |  ||  ||     | | |||||| || | |     ||| ||| | | |   | || | | || || |         ||     || |   | ||   ||||||||| | |||     ||| |||||||  |||||| |||||||||||||||| || |||||| ||||| |||||||  | |||||||||||||||||| |||
---------------------------gtaatcag--aagttacaattgatcctcttgttaatg-actaaaattattttttccactgttatcatagaaattcatataaaccaatttttggcttaaattttgtcatgtgcagGAACTATGGCAAAGGAGAGTTGAGAAGTACTGGGATCTCTTGAGTCCAAAAATCACATCAAACACATTGAGGAATATTATGGATATGAAAGCAAACATGG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 6
gtaatttgaggcagtacccccttgtctgcaattttttagtttgtaaagatcctttttgttagtgc-attgtggatatgtttgcaaatacaacacacacatacaaaagtgtgggcttacaaattga---tggtgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAGATTACATCAGACACACTGAGGAACTTGATGGATATGAAAGCAAACTTGG
|||||  ||      |     |  ||  ||   | |||     ||||  |  |||||     ||  |   | || || |||| | |   || | | |  |  | | |       ||     || |   | ||    |||||||| | |||     ||| |||||||  |||||| ||||||||||| |||| || |||||| ||||| |||||||  | |||||||||||||||||| |||
gtaatcagaaattacaat---tgatcctca---tgttaacgactaaaattaatttttccccctgttagcatagaaat-tttgtataacaaaaatataattttagatgaaccaatttttggcttaaattttgtcatctgcagGAACTATGGCAAAGGAGAGTTGAGAAGTACTGGGATCTCTTGAGTTCAAAAATCACATCAAACACATTGAGGAATATTATGGATATGAAAGCAAACATGG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 5
gtaatttgaggcagtacccccttgtctgcaattttttagtttgtaaagatcctttttgttagtgcattg-tggatatgtttgcaaatacaacacacacatacaaaag-tgtgggcttacaaattgatggtgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAGATTACATCAGACACACTGAGGAACTTGATGGATATGAAAGCAAACTTGG
|||||| ||    | |     || ||||   | ||||| || |      |  || |||| |||  ||   |   |    |  ||||   | ||   | ||| | | | | | ||||||    ||| |  |||||| |||||| | |||      || ||||||| |||||||||||| ||| ||||||| ||  | ||  ||||| |||||||  ||||||| |||||||||||| |||
gtaattggaatttgcaatttattctctggtttgttttaattag--gttcttgttcttgtgagtatataaattattgaactaacaaaggtaccat-tagataaataggctattggcttaactcttg-tcctgtggtacagGAACTATGGCAAGGAAGAGTTGAGAATTACTGGAATCTATTGGGTCCAAAAATCTCGTCGAACACAGTGAGGAATGTGATGGACATGAAAGCAAACATGG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaatttgaggcagtacccccttgtctgcaattttttagtttgtaaagatcctt--tttgttagtgcattgtggatatgtttgcaaatacaacacacacatacaaaagtgtgggcttacaaattgatggtgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAGATTACATCAGACACACTGAGGAACTTGATGGATATGAAAGCAAACTTGG
                                      || | || | | || |   || |  ||  ||||    |       ||||   || || ||    | |    ||    | | |  ||  |  | |  | |||||| |||||| |||||| || || | ||| ||| |||||||||||||||  ||   |||||| ||| |||||||| | ||||| |||||||||| | |||
--------------------------------------gtatatagaaacccataacttctctgtttattgcaactg-----acaaac-taagac-catgggctattaagtcacatcatatgtttcttat-tcatacagGAACTTTGGAGGCAGAGAGTAGATACTTATTGGGATCTCTTGAGTCCAAGAATCGAATCAGATACAGTGAGGAACATAATGGACATGAAAGCAAGCATGG

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|110712757|gb|EE088080.1|EE088080
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGA-ATATTTGAGAAAGAC-CN                         GAAATTTGGATGCAGAGGGTTGA
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGA
EST: gi|110699783|gb|EE077083.1|EE077083
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|56409526|gb|CX017778.1|CX017778
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|27580186|gb|CB002881.1|CB002881
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|34545569|gb|CF513801.1|CF513801
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|34545484|gb|CF513716.1|CF513716
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|56409685|gb|CX017937.1|CX017937
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|71858970|gb|DT008025.1|DT008025
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|351021835|gb|FQ437220.1|FQ437220
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|56409742|gb|CX017994.1|CX017994
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|71886266|gb|DT035321.1|DT035321
EST:     CTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|349830601|gb|FQ416899.1|FQ416899
EST:     ACGTCTAGCTGATTTTGGCTAATTCAAA-GAAATATTTGAGAAGGACACG                         GAAGTTTGGAT
genomic: ACGTCTAGCTGATTTTGGCTA-TTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGAT
EST: gi|110716290|gb|EE091140.1|EE091140
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|110689293|gb|EE065391.1|EE065391
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAA-G
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|110715719|gb|EE094088.1|EE094088
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|110694546|gb|EE071749.1|EE071749
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|110357653|gb|EC921295.1|EC921295
EST:     TGAGAA-GACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: TGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
EST: gi|110715151|gb|EE092872.1|EE092872
EST:     CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACG                         GAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG
genomic: CACGTCTAGCTGATTTTGGCTATTCAAAAGACATATTTGAGAAGGACACGgtaatttgag ... tgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatacaacacacacatacaaaagtgtgggcttacaaattgatggtgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAGATTACATCAGACACACTGAGGAACTTGATGGATATGAAAGCAAACTTGG
                               ttacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgaggcagtacccccttgtctgcaattttttagtttgtaaagatcctttttgttagtgcattgtggatatgtttgcaaatacaacacacacatacaaaagtgtgggcttacaaattgatggtgtggtgcagGAAGTTTGGATGCAGAGGGTTGAGAGTTACTGGAATCTCTTGAGTCCAAAGATTACATCAGACACACTGAGGAACTTGATGGATATGAAAGCAAACTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA