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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaattattcaaatcccatttagtatgcaaatatgtacctcttttgttctgtagttagagtttgtcc...

Basic information

species Vitis vinifera
transcript Vv09s0002g03410.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g03410.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G21460.1 (Glycine max), 5'ss of exon 3
AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaattattcaaatcccatttagtatgcaaatatgtacctcttttgttctgtagttagagtttgtcc----
||||| | | ||  |||||  | | ||| ||||| |||||||| |||||||| |||||||| |||||||||||  | |||||||| ||||| || ||||||||||||||| | || ||||||||||||||||||  ||  |    || | ||| | |||   | |   |  || |  | |  |  | |       ||       
AGAAATCCAATAAGGGTTTATTGGTTGGAAGTGGGGAATATACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGAGATGTGCCGTGGCAgtaagcatcttatcaatgtggatctgatgcatttttatctt----attctattcaatattatattccatgactatagtttgatacaatattgccatgcagtgga

upper sequence: Vv09s0002g03410.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G01800.1 (Glycine max), 5'ss of exon 3
AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaattattcaaatcccatttagtatgcaaatatgtacctct--tttgttctgtagttagagtttgtcc--
||||| | | ||| |||||  | | ||| ||||| |||||||| |||||||| |||||||| |||||||||||  | |||||||| ||||| || |||||||||||| || | || ||||||||||||||||||  ||  |    || | ||| | |||   | |   |  || |  |||| |   | |  |     ||     
AGAAATCCAATACGGGTTTATTGGTTGGAAGTGGGGAATATACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGAGATGTGCCGTGGCAgtaagcaccttatcattgtggatctgatgcatttttatctt----attctattcaatattatattccatgactatagtttgatacattgccatgcagtggagta

upper sequence: Vv09s0002g03410.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G02350.1 (Glycine max), 5'ss of exon 4
AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaattattcaaatcccatttagtatgcaaatatgtacctcttttgttctgtagttagagtttgtcc----
||||| | ||||| || ||  | ||||| ||||| || ||||| |||||||| |||||||| |||||||||||  | |||||||||||||| |||||||||||||||||| | |||| |  |||| ||| | |   ||||||  | |   ||| | |||   | |||       | |   ||   | ||   || ||       
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTATACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcactatcaatcttatgtact---attatttta-ttttattcaatattatattatactatattgtacctcaccacttgatgtgtgaggacca

upper sequence: Vv09s0002g03410.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G43050.1 (Glycine max), 5'ss of exon 4
AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaat--tattcaaatcccatttagtatgcaa-atat-gtacctcttttgttctgtagttagagtttgtcc
||||| | ||||| || ||  | ||||| ||||| || | ||| |||||||| |||||||| |||||||||||  | |||||||||||||| |||||||||||||||||| | || | |  || | ||||| |   ||  ||||  | ||     || |||   | |||| |||||||     ||  |  || ||      |  
AGAAAGCAATTACGGGGTTATTGGATGGAAGTGGAGAGTTTACTCTTGTTTATGAGGATAATGAAGGAGACAGGATGCTTGTTGGGGATGTGCCATGGCAgtaagcatcttatcagtatcaattttatgcactattattttattttattcaatactattatattatatattgtacctcaccactt--gatgtgaggaccaat--

upper sequence: Vv09s0002g03410.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G16500.1 (Arabidopsis thaliana), 5'ss of exon 3
AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaattattcaaatccc--atttagtatgcaaatatgtacct-cttttgttctgtagttagagtttgtcc
||||| |||| | ||| ||  | |||||||  || |||| |||  |    || || || || ||||| ||||   | |||||||||||||| ||||||||||||| ||||   | |  |   |    || || | | | | |    | |   |||   |     |  || || |  |    |||||    ||  | |      
AGAAACCTATCATTGGATTATTAGATGGGAAAGGAGAATTTACTTTAACCTATGAAGACAATGAAGGGGACAAGATGCTTGTTGGGGATGTTCCATGGCAgtaagaatcttttccccttttgttctctgaatctgattcagtgttttgcagaattagattcttgatcatataacaacaaaagttctcagcttttaatcaa---

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|110422054|gb|EC988366.1|EC988366
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
EST: gi|110418706|gb|EC984872.1|EC984872
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
EST: gi|30251350|gb|CB969083.1|CB969083
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACCCGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
EST: gi|30251265|gb|CB968998.1|CB968998
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACACG
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACG
EST: gi|30251355|gb|CB969088.1|CB969088
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACCCGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
EST: gi|30251271|gb|CB969004.1|CB969004
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGA
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGA
EST: gi|161721537|gb|FC069747.1|FC069747
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
EST: gi|110386232|gb|EC950813.1|EC950813
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAACT
EST: gi|156736126|gb|EV240247.1|EV240247
EST:     TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCA                         CATGTTCGTGAACACNGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAAAC
genomic: TACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatct ... tcacatgcagCATGTTCGTGAACACGGTGAAGAGGTTGCGCGTGTTGAAGAGCTCTGAA-C

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAACTATTACTGGTTTGCTCGATGGGAGTGGCGAATATACGCTTGTTTACGAGGATAACGAAGGAGACAGAGTCCTTGTTGGGGATGTCCCATGGCAgtaagcatctaaccactgtggatctgatgcatttcaattattcaaatcccatttagtatgcaaatatgtacctcttttgttctgtagttagagtttgtcc

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaata