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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccttcctacatctttatcttcagagcatgttgaaactagaatactaaagtagtaagaattgttcatctgatctgtgaatacaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG

Basic information

species Vitis vinifera
transcript Vv07s0129g00180.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G118919_T01 (Zea mays), 3'ss of exon 1
gtccttcctacatctttatcttcagagcatgttgaaactagaatactaaagtagtaagaattgttcatctga---tctgtgaatacaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
                        | |   |||     |  || |   |  ||  |     ||    ||||    ||  |  || | ||||    |  |     ||||||||||  ||||||| ||  | |||||||| ||  ||||||| ||| || |||| ||||||| |||||||||||| || ||||| ||||| ||||| |
----------------------gtgggtgggttagcgttgaaagatgtagataa-atcgtctgcatttctggagctcctttgat-cgatttcacgctgcgattcagGTAATGGCGAGATCTTCGCCGCTCGACAAGCACACTTTGGTGAAGCACCTACGAACAACATTTGATGAAGTTGTTGCGGTCACCGGCGATGGCACAAACG

upper sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G22420.1 (Glycine max), 3'ss of exon 3
gtccttcctacatct-ttatcttcagagca-tgttgaa---actagaatactaaagtagtaaga-attgttcatctgatctgtgaat-acaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
|| |||| ||||  |  ||| |  | | || | ||  |   |||  | |  | |||  | ||    ||| |  | | |    |  ||     ||  |||    | ||  ||| ||||||||||| |||||| | ||||| |||||||||||||||||| |  | ||||||||||| |||||||| ||||| || ||||||||||||||||
gtgcttcatacacttgctatatgaataacaatatttgattgactcaattcttgaagagggaaatcgttggtgctttaaataatatattgtggttaattttgttttaa--gGTTATGGCTCGATCCTCACCTCTAGACAAACATACACTGGTGAAACACCTTCGTACCACATTTGGGGAAGTTGTAGCTGTAACTGGTGATGGAACAAATG

upper sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 3
-------gtccttcctacat-ctttatcttcagagcatgttgaaactagaatactaaagtagtaagaattgttcat--ctgat-ctgtgaatacaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
        | ||| ||  || | |||| ||  ||     |    ||||   || | | | |  | || || ||  |   | || || | | |   | | |||    |    ||||| ||||||||||| |||||||| ||||| || |||||||||||||||||  | ||||| ||||| ||||| || ||||| || ||||||||||| ||||
gtgccatatactttctgtatgcattatattttgactccttcagtactact-taatcatgca-catgatttatttgtggttcatactttaactgacagtgtttgattccttttagGTTATGGCTCGATCCTCACCTTTAGACAAACACACACTGGTGAAACACTTGCGTACCACTTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATG

upper sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 4
gtccttcctacatct-ttatcttcagagcatgttgaaactag--aatactaaagtagtaaga--attgttcatctgatctgtg-aatacaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
|| |||| || | ||  ||| |  | | ||| ||  |   |   ||| || ||  ||  |||  |||| |  | | |    |  |||    ||  ||| |  | ||  ||| ||||||||||| |||||| | ||||| |||||||||||||||||| || | ||||| || || ||||| || ||||| || ||||||||||||||||
gtacttcatatacctgctatatgaaaaacatctttgattgattcaattcttaaacagggagataattggtgctttaaataatataatgtgtttgattttcttttaa--gGTTATGGCTCGATCCTCACCTCTAGACAAACATACACTGGTGAAACACCTACGTACCACGTTCGGGGAAGTCGTAGCTGTAACTGGTGATGGAACAAATG

upper sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 3
gtccttcctacatctt-tatcttcagagcatgttgaaact---agaatacta--aagtagtaagaattgttcatc--tgatctgtg--------aatacaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
|| |  | || | ||| ||   |   |  || ||   |||     | |||||   | |  ||   ||  || ||   || |  ||         || |  | | |||    |    ||||| ||||||||||| |||||||| ||||| || ||| |||||||||||||  | || || ||||| ||||| || ||||| || ||||||||||| ||||
gtgccacatataccttctaatatgcaattatattttgactccttcagtactacttaatcatacacataatttatttatggttagtactttaactaacattagtgtttgattccttttagGTTATGGCTCGATCCTCACCTTTAGACAAACACACATTGGTGAAACACTTGCGTACTACTTTTGGGGAAGTGGTAGCTGTAACAGGTGATGGAACTAATG

upper sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 3
gtccttcctacatctttatcttcagagcatgttgaaactagaatactaaagtagtaagaattgttcatctgatctgtgaa-tacaatttttttc----ccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
                        | || | |||   |  |||  |||||| | | |   || ||  | |  | | ||||  | ||  |||        | |  | |||| |||||||| ||||||||  |||| ||||||||||| |||||||| ||||| || || |||| ||||||||||||||| || || |||||||||||||
------------------------gtgctttttgtttcatgaa--ctaaag-acttaattttttttgtttagtttttgaaacataacctttcctatgttcttatacagGTGATGGCTCGTTCTTCACCAATGGATAAGCATACACTTGTGAAACAGTTAAGGACAACGTTTGATGAAGTTGTTGCTGTCACTGGAGATGGAACAAATG

upper sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 3
gtccttcctacatctttatcttcagagcatgttgaaactagaatactaaagtagtaagaattgttcatctgatctgtgaatacaa-tttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
                         | | | |  | | |   ||| |       |  |  || || ||  |   |   |  | || |||||||   ||  | |||| |||||||| ||||| ||  |||||||||||||||||||||| || || || || || |||| |||||||||||||||||| || || || ||||| |
-----------------------gtaacttttcaagatttagatattt------tttgctttcttgataagtctttaaaccataacttttttttttcttgacagGTCATGGCTCGTTCTTCCCCAATGGACAAGCATACACTGGTGAAGCAGTTGAGGACTACTTTTGATGAAGTTGTTGCTGTGACTGGCGACGGGACAAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtagtaagaattgttcatctgatctgtgaatacaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG
                                  caatttttttcccctc  CT-rich tract
                            tgaatacaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccttcctacatctttatcttcagagcatgttgaaactagaatactaaagtagtaagaattgttcatctgatctgtgaatacaatttttttcccctcaatagGTAATGGCTCGATCTTCACCTTTGGACAAGCATACACTGGTGAAACACTTAAGAACCACATTTGGTGAAGTTGTTGCTGTGACCGGTGATGGAACAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA