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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT

Basic information

species Vitis vinifera
transcript Vv18s0001g13090.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 3
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
                                                   ||| |    |    |    || ||  || |    | ||  |||| |  ||| |    || |  | ||     ||  ||   ||     |   ||   | | ||    || ||    |||     | ||  |||    ||||||||||||| ||||| || |||||||| ||||||||||||||| |||||||||||||||| ||||| ||||| ||||| ||| | ||| | ||||| |
--------------------------------------------------gtaagtcgtagtttattattttaatattttcattttatgaacatgttcttttcc--tgttgtgctaagatctgatt-tattggatccctggtggtcactattgtct--ctaattctttgt----cgttggagtt-gccagGTTGATCCAGTAGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTACTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT

upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 3
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
                                                   ||| | |  |    |    || ||  || ||   | ||  |||| |  | |       ||  | ||    |     ||    |     |    |   ||| ||    || ||    |||     | ||  |||    ||||||||||||| ||||| || |||||||| ||||||||||||||| ||||||| |||||||| ||||| ||||| ||||| ||| | ||| | ||||| |
--------------------------------------------------gtaattcatagtttattattttaatattttctttttatgaacatgttcttgtcttg---ttgtgctaacatctgatttattttatccctggtgatcactgttgtct--ctaattctttgt----cgttggagtt-gccagGTTGATCCAGTGGTTTACAATATGTTGCATGAAGATCCTGGTAATATCAGCTATTCAGCTGTTGGTGGCTTATCTGATCAGATCAGGGAATTGAGGGAGT

upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 3
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatg-att--attttcaacatttta-gttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
                                                         |||    ||    ||| || ||| ||| ||| |  ||  |||  ||||    |||   | ||| |||    |  | ||||  |      ||||| | ||  |||  || |  | | || |||   |    || | ||||||||||||| ||||| || ||| |||| || |||||||||||| |||| ||||| ||||| ||||| ||||| ||||| ||  | ||| | |||||| 
---------------------------------------------------------agtaagttt----ttgctgtttattccttttagatatctatttgatttggtgcatgcgatgtttgtgttctttctgaaagtcatgtcctagtttttttgtgtctgatggtcaa-tatgatatatcgtgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCCGATCAGATAAGGGAATTGAGGGAA-

upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 3
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
                                            |  |       ||| | || | |||     |  ||| |  |||||||  |   |  ||     || | | || ||  |  ||  ||||  |         |||  |||  |||  || |  | | || | |   |    || | ||||||||||||| ||||| || ||| | || || |||||||||||| |||| ||||| ||||| ||||| ||||| ||||| ||  | ||| | |||||||
-----------------------------------------gtaagtttttctgtttatttgcttcaga-----tatttatttaatttggtgtt--cttgttgggctatctgatttggtttctttctgaaaatcatgtcctagtttttcgtg--tctgatggtcaa-tatgatctatcgcatgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCTGATCAGATAAGGGAATTGAGGGAAT

upper sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
                                                                                     || ||   | || || ||    | |   ||| || | | |   |||          |    | | | ||| |    ||    || ||| ||||         ||||||||||| || || || |||||| | ||||| || ||||||||| | |||||||||||||| || ||  ||   || ||||| ||||||||  | || |
-------------------------------------------------------------------------------------ttaggatcttat-atgtttgtgagtc--gttggtaaaatttccaaatatcttctccgctgatttttcgttttgtgcatttg-tgcgct-tgattcgtgcggttagGTTGATCCCGTAGTGTACAACATGCTTCACGAGGACCCTGGTAATATTAGCTACTCAGCTGTTGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGT

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|30128746|gb|CB914085.1|CB914085
EST:     TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAA                         GTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC
genomic: TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAAgtaagttacc ... tgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC
EST: gi|30136830|gb|CB922168.1|CB922168
EST:     TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAA                         GTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC
genomic: TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAAgtaagttacc ... tgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC
EST: gi|294966241|gb|GW839464.1|GW839464
EST:     TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAA                         GTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC
genomic: TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAAgtaagttacc ... tgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC
EST: gi|71859476|gb|DT008531.1|DT008531
EST:     TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAA                         GTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC
genomic: TGGTTCTTGATATGACAACACTCACAATCATGCGAGCTCTTCCACGTGAAgtaagttacc ... tgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
                     tcctgat  putative branch site (score: 3)
                                            atgtttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA