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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattcccttcatctagttagaagtaaagttgaatgttgaggtcacgactgaaagtataaatttcttttcccttatatgacattgtttttattggatcatatgggtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC

Basic information

species Vitis vinifera
transcript Vv13s0106g00620.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 3
gtgagattcccttcatctagttagaagtaaagttgaatgttgaggtcac-gactgaaagtataaatttcttttcccttatatgacattgttttta-ttggatcatatgg-gtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC
                      |||  |    |||| |  ||  || ||  | ||  | ||       |  ||  ||||  ||| ||| |  | | |||  |  ||||  || |  |||  ||| || || |||||||| ||||| | ||||||||| ||||| ||||||||||| || ||||| || || |||||||| ||||||||||||||||||||||| 
----------------------agagctgttattga-tactggtgtaactaattgttaatacttggaccaattatcttac-tgatattttactgacttgttttttatgttgtgtttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCAT

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G20970.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagattcccttcatctagttagaagtaaagttgaatgttgaggtcacgactgaaagtataaatttcttttcccttatatgacattgtttttattggatcatatgggtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC
|| || ||    |  | |   | | || || | | ||||                 |||     ||  |||||   | | | |  |  |   ||    ||| | |||||    ||  ||||||| |  || ||||| || || |  ||||||||||| |||||||| || || ||||||||||||||  ||||||| || || ||||| ||||||||||| 
gtaagtttatacttctttgagttgtagcaatggtcaatg-----------------agtcctgtttctttttcttgtctcttaagtcttaagtaa-aaatcctttgggtgggtttaatcagGGAAAGCGGTATAGTGAAGCTGAGGATGCAAGGAGCTTGTAGTGGTTGTCCGAGCTCATCTGTTACTTTGAAATCGGGAATCGAAAACATGCTGATGCAT

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G20970.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgagattcccttcatctagttagaagtaaagttgaatgttgaggtcacgactga-aagtataaatttcttttcccttatatgacattgtttttattggatcatatgggtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC------
                   |||   | |    ||||  ||||  |  | |    |  |||     ||  |||||   | | | |  |  |   ||    ||| | |||||    ||  ||||||| |  || ||||| || || |  ||||||||||| |||||||| || || ||||||||||||||  ||||||| || || ||||| |||||||||||       
-------------------gtttatacttct-ttga--gttgtagcaatggtcaatgagtcctgtttctttttcttgtctcttaagtcttaagtaa-aaatcctttgggtgggtttaatcagggaaagCGGTATAGTGAAGCTGAGGATGCAAGGAGCTTGTAGTGGTTGTCCGAGCTCATCTGTTACTTTGAAATCGGGAATCGAAAACATGCTGATGCATTATGTA

upper sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G51390.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagattcccttcatctagttagaagtaaagttgaatgttgaggtcacgactgaaagtataaatttcttttcccttatat-gacattgtttttattggatcatatgggtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC
                                        | || |    | |  |  || ||     | |||  | | || |   || | |||||   | | |||  ||||   |  | ||||| || || ||||| || || | |||||||||||| ||||| || || || || |||||||||||  ||||||| || ||||| |||||||| ||||| 
---------------------------------------gtaagttttttatttgagttaaaagcaaatgttcaataagatcggatttatctttatcaaagc-tatttgttt---tggttagGGAAACTGGTATAGTGAAGCTTAGAATGCAAGGAGCTTGTAGCGGTTGTCCAAGTTCATCTGTTACTTTGAAATCCGGAATTGAGAATATGCTTATGCAT

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|110721131|gb|EE097777.1|EE097777
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
EST: gi|30128878|gb|CB914217.1|CB914217
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
EST: gi|349819125|gb|FQ412019.1|FQ412019
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTG
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTG
EST: gi|349813184|gb|FQ411424.1|FQ411424
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTA
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTA
EST: gi|110417947|gb|EC984052.1|EC984052
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
EST: gi|110413185|gb|EC978962.1|EC978962
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
EST: gi|349820680|gb|FQ408509.1|FQ408509
EST:     CCAGCATTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGGATAGTTTAACTAAAAATGCAAGGAGCATGTA
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTA
EST: gi|349824783|gb|FQ414641.1|FQ414641
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
EST: gi|110426203|gb|EC992603.1|EC992603
EST:     CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCC                         GGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC
genomic: CCAGCAGTTCAAGATGATGGTGGGGACATCGAGTATCGGGGATTTGATCCgtgagattcc ... acttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttcccttatatgacattgtttttattggatcatatgggtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC
                                          tttacttcctc  CT-rich tract
         ttatatgacattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattcccttcatctagttagaagtaaagttgaatgttgaggtcacgactgaaagtataaatttcttttcccttatatgacattgtttttattggatcatatgggtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT