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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatttggcttcttgccccattgatcatatgctttaatgttaggggataagttggtgaattatggactctgggtgggaaaaggaagagaaatata...

Basic information

species Vitis vinifera
transcript Vv00s0264g00020.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0264g00020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA01G36760.1 (Glycine max), 5'ss of exon 3
TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatttggcttcttg--ccccattgatcatatgcttt-aatgttaggggataagttggtgaattatggactctgggtgggaaaaggaagagaaatata
||| || ||||||||||| |||||||| ||||| || |||||||| |||||||||||||||||||||||||| || |||||||| ||| |  | ||| |||||||  | |   |||   |    |  ||    |  ||||||  ||| | |  | | | || |  ||||   |  |    || | |    | | |    |   
TGGTGCCATATCAGGAGCCGTTTTCTCCATTGAAGTGTTTGAATCCTCTCTTGTTCTCTGGCAATCTGATGAATCTGGGATTGGTTGTGTCTTATACTTGgtgagttactcacctttcagaatgcagttctctaggtgcttttgatgct-gttgttcaattag--aattggagttttaccgtagtattttgcataatccttgg

upper sequence: Vv00s0264g00020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA11G08540.1 (Glycine max), 5'ss of exon 2
TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatttggcttcttgccccattgatcatatgctttaatgttaggggataagttggtgaattatggactctgggtgggaaaaggaagagaaatata-----
||| || ||||||||||||||||| || ||||| || |||||||| |||||||||||||||||||||||||| || |||||||| ||| |  | ||| |||||||    |  ||||   |  | |  ||  | |  ||| ||||  ||  | | | || |  ||||   |  |    || | |    |   |    | |      
TGGTGCCATATCAGGAGCTGTTTTTTCCATTGAAGTGTTTGAATCCTCTCTTGTTCTCTGGCAATCTGATGAATCTGGGATTGGCTGTGTCTTATACTTGgtgagttgctcagctttcagggcaaaggacaaaa--cttaaatgc-agttgttcaattag--aattggagttttaccgtagtattttgcgtaatcctttgatgca

upper sequence: Vv00s0264g00020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA16G23050.2 (Glycine max), 5'ss of exon 4
TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatttggcttcttgccccattgatcatatgctttaatgttagggg-ataagttggtg------aattatgga---ctctgggtgggaaaaggaagagaaatata----------------------------------------------------
 || || ||||||||||||||||| || ||||| || ||||||||||| |||||||| ||| ||||||| || || || ||||| ||| |  | ||| ||||||| || |    |   |  |   || |  |  |  |  ||  |  |    |||| ||| |       |||| | ||   || ||  |||    | ||      ||                                                       
AGGTGCCATATCAGGAGCTGTTTTTTCCATTGAAGTTTTTGAATCTTCCCTTGTTCTTTGGAAATCTGACGAATCTGGAATTGGGTGTGTCTTATACTTGgtgagtaagtgacatggctttcattttcaagaccttgtcaaaaataggatatataaattgctactacacaattcttgagttctttgcttggccccatgagattttattgtcattttcactagcaagttgtgtagtctaatcattttaagttatgtaatgcag

upper sequence: Vv00s0264g00020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G05000.1 (Glycine max), 5'ss of exon 2
TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatttggcttcttgccccattgatcatatgctttaatgttagg-ggataagttggtg---aatta-tggactctgggtgggaaaaggaagagaaatata
 || || ||||||||||||||||| || ||||| || ||||||||||| |||||||| ||| ||||||| || || || ||||| ||| |  | ||| |||||||  | |    |  ||  |   || |  |  |  |  ||| |  |    | || ||| |    ||||  ||   ||| |   |  | | ||  ||       
AGGTGCCATATCAGGAGCTGTTTTTTCCATTGAAGTGTTTGAATCTTCCCTTGTTCTTTGGAAATCTGACGAATCTGGAATTGGGTGTGTCTTATACTTGgtgagttagtcacttggttttcattttcaagaccttgtcaaatatgggatatagaaattgctacacaattgctgagttcttgagagttataagattaggc-----

upper sequence: Vv00s0264g00020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT4G35840.1 (Arabidopsis thaliana), 5'ss of exon 2
TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagc-aatttggcttcttgccccattgatcatatgctttaatgttaggggataagttgg-tgaattatggactctgggtgggaaaaggaagagaaatata
|||||| || || ||||||||||||||||| || |||||||| || ||||||||||| ||| ||||| |||||||| |  |||||||||| |||||| ||||||||  |  |      |||  | | | |||   |   ||  | |   |   | | | |     ||| | |  ||| | |       |             
TGGAGCCATTTCGGGAGCTGTTTTCTCTATCGAAGTCTTTGAGTCATCTCTTGTTCTTTGGAAATCTAATGAGTCACGTTTTGGATGTCTCCTCTACTTGgtgagctgagatcttcatttgaactactcatctgctctgtttttttccagatttgattcgaactgattcttgtttcttgttaatctttgtgtag--------

upper sequence: Vv00s0264g00020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT2G17730.2 (Arabidopsis thaliana), 5'ss of exon 2
TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaat-----ttggcttcttgccccattgatcatatgctttaatgttaggggataagttggtgaattatggactctgggtgggaaaaggaagagaaatata
|||||| || || ||||||||||||||||| |||||||||||||| ||||| | ||||||| |||| |||||||| ||  | |||||| | |||||| ||||||||||      |||   | ||     | |    ||    |||    |  || ||| |||   |   || || | | |  |||                    
TGGAGCCATTTCGGGAGCTGTTTTCTCTATCGAGGTCTTTGAATCATCTCTGGATCTCTGGAAATCCGATGAGTCGGGTTTCGGATGTTTTCTCTACTTGgtgagcaacattacttgctctgttttttaagtagctatgaagtttggaatgtggtgattagtgtttcttttgtgaattttttgtgtag-----------------

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|110383407|gb|EC947779.1|EC947779
EST:     TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTG                         ATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
genomic: TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
EST: gi|110714538|gb|EE091563.1|EE091563
EST:     TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTG                         ATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
genomic: TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
EST: gi|30304420|gb|CB981214.1|CB981214
EST:     TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTG                         ATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
genomic: TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
EST: gi|34320290|gb|CF373044.1|CF373044
EST:     TTGTTCTCTGGCAATCTGATGAGTCAGGGATGGGATGTCTGCTCTACCTG                         ATTGATGTTATNGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
genomic: TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
EST: gi|110721740|gb|EE097361.1|EE097361
EST:     TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTG                         ATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
genomic: TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
EST: gi|110374711|gb|EC939634.1|EC939634
EST:     TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTG                         ATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
genomic: TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
EST: gi|110430291|gb|EC996837.1|EC996837
EST:     TGGATGTCTGCTCTACCTG                         ATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTTGTTCGTGAGAGGATC
genomic: TGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
EST: gi|30304486|gb|CB981280.1|CB981280
EST:     TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTG                         ATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC
genomic: TTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatt ... aattgtacagATTGATGTTATTGTAAGCCTGCTAAGTGGTAGACTCGTTCGTGAGAGGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGCAATATCAGGAGCTGTTTTCTCTATTGAGGTCTTTGAATCTTCTCTTGTTCTCTGGCAATCTGATGAGTCAGGGATTGGATGTCTGCTCTACCTGgtgagcaatttggcttcttgccccattgatcatatgctttaatgttaggggataagttggtgaattatggactctgggtgggaaaaggaagagaaatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agagaaa